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The Rebel Flagship

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Flagship Whole

The Rebel Flagship is by far the most powerful vessel in the Rebel Fleet, and serves as the game's final boss, located in The Last Stand sector. Despite the Rebel Flagship being found in The Last Stand sector, you may be able to find its weaker prototype in a Rebel Stronghold sector, as part of a rare event. Defeating this prototype for the first time will unlock the Federation Cruiser and its quest. Although you only need to find it once to unlock the quest, it can be found more than once, acting as a normal ship with much greater rewards.

You start in a sector with multiple systems being overtaken by the rebels. Jumping to these starts a battle with a strong Rebel Elite ship. There are Repair beacons where you can get a one-time 15 hull repair along with a fair amount of resources and scrap. The base gives you no repair, and is the primary target of the Rebel Flagship.

In addition, the silhouette of the Rebel Flagship is visible hovering around a beacon, marking its location in the same way your location is. Every 3 jumps you make, it will jump closer to the Federation base. If it reaches the Base and remains there for 3 turns, the game will end, as it is proposed that the base is destroyed, eliminating the chance for Federation victory.

Your primary goal is to make it to the Flagship, fighting through its three increasingly difficult stages to destroy it, thus ending the Rebel advance. With each stage that you beat, the rebel flagship will jump away, nearing the fleet. It will quickly head back towards Federation base on its next jump, however; so don't take it as incentive to explore the sector.

Contrary to popular belief, it is safe for your ship to FTL jump away from the boss at any time. Depending on the map, you may be able to flee once or twice.

Global behaviorEdit

At the end of the first and second stage, the flagship will lose a part of its hull along with the rooms, systems and weapons in the corresponding location. Other systems will be installed on the next stage, thus changing its behavior dramatically.

On the second and third stage, the flagship has a special ability called "Power Surge" which will be triggered periodically and cannot be disabled by the player, much like Environmental Hazards.

Hull and system damage of the Rebel Flagship will be repaired on the next stage. Breach and fire will also be cleared. Only the crew is persistent through each stage; crew members killed are not replaced on the next stage.

Unlike most manned fights, killing the entire enemy crew won't win the fight. Instead, a message will pop up pointing out the AI took control of the ship. The flagship will then behave like most automated ships: systems are all progressively repaired at a set rate, except those with a breach in their room.

The flagship's weapons behave like artillery weapons, meaning that they have their own systems in separate rooms, which can also be manned. These rooms are also isolated from the main structure of the ship (with an exception on hard mode).

Although the flagship uses a Missile Launcher, it does not consume any missiles and will therefore never run out of ammunition.

After the flagship jumps away, the player will receive a small amount of scrap, fuel, drone parts, and/or missiles. Also, there is a slight chance for a random weapon or augment being dropped.

Flagship variationEdit

On easy mode with Advanced Edition Content disabled, the flagship only has 3 layers of shield instead of the usual 4 (which means the Shield system level is 6 instead of 8). This applies for all three stages.

On hard mode, two additional rooms link the Laser and Missile ones to the main section of the ship. This implies the crew member manning the weapons can be replaced and the systems can be repaired by the crew.

1st StageEdit


The Final Boss, 1st stage (transparent rooms only exist on Hard mode)


Like any other ship, the flagship consumes 1 drone part to deploy its hacking drone. This means it is possible (yet difficult) to avoid being hacked entirely by shooting down 10 hacking drones in a row with a Defense Drone.


Numbers in parenthesis are system levels.


Dodge RateEdit

Assuming cockpit and engines are unharmed and the engines are fully powered. Based off system health of the engines and cockpit.

  • Base Dodge rate: 10%
  • While fully manned 20% (Enemy crew is unskilled regardless of difficulty)
  • If unmanned 8%

Note: This assumes the Flagship operates just like a player ship. Exploration using the editor suggests the ship automatically receives the fully manned bonus without crew. Granted, the player controlled Flagship had advantages the Boss Flagship did not have (Auto repair was on at all times while this only happens to the Boss Flagship if the entire crew is killed.).


It is not recommended that you try and kill ALL the enemy crew, as even if you do the advanced ship AI takes over repairing systems and piloting the ship by itself. The best thing is to leave one crew member alive, preferably in the Triple Laser room where he can not repair the rest of the ship (except on Hard difficulty). This will make the later two stages much easier as no systems will be repaired and the teleporter will be useless for the enemy crew. Be warned that any enemy crew that is mind controlled when the ship jumps to the next phase is considered an enemy. Just like any friendly boarders you have on the enemy flagship, they will be purged for the next round. This potentially leaves the ship unmanned and gives the AI control at the start of the next phase, but can be used to your advantage if there is more than one enemy crew left.

2nd stageEdit


The Final Boss, 2nd stage (transparent rooms only exist on Hard mode)

With its cloaking (and hacking) gone, the boss now relies on its drone system along with its power surge, which spawns more drones.


  • Hull : 22
  • Reactor : 44
  • Crew : The remaining crew from the previous stage (Minus those in the rooms that were removed).
  • Drone parts : 10

Like on the previous stage, it is possible to avoid being boarded entirely by shooting down the Boarding Drone until the flagship runs out of drone part. Since it uses 4 drones at once, this can happen quite quickly.

Note that drones from the Power Surge don't consume drone parts.


Numbers in parenthesis are system levels.

The Boss Ion was lost during the previous battle.



The Hacking, Door and Cloaking systems were lost in the previous battle.

Power SurgeEdit

  • Deploys six extra drones (randomly split between Beam and Combat) for approximately 5 seconds.

These appear even if the drone control system has been destroyed. Hacking the drone system does not stun the power surge drones (even when the system is online).

Dodge rateEdit

Assuming cockpit and engines are unharmed and the engines are fully powered. Based off system health of the engines and cockpit.

  • Base Dodge rate: 15%
  • If fully manned 25% (Enemy crew is unskilled regardless of difficulty)
  • If unmanned 12%

Note: This assumes the Flagship operates just like a player ship. Exploration using the editor suggest the ship automatically receives the fully manned bonus without crew. Granted, the player control Flagship had advantages the Boss Flagship did not have (Auto repair was on at all times while this only happens to the Boss Flagship if the entire crew is killed.).

Final stageEdit


The Final Boss, 3rd stage (transparent rooms only exist on Hard mode)

With its drones gone, the flagship now relies on its Zoltan shield, power surges, and boarding crew to overcome the player.


  • Hull : 20
  • Reactor : 32
  • Crew : The remaining crew from the previous stage.

The flagship's Zoltan Shield has 12 health points.


Numbers in parenthesis are system levels.

The Boss Beam was lost during the previous battle.


The Drone system was lost in the previous battle.

Power SurgeEdit

One of the two :

  • Shoots 8 laser shots simultaneously,
  • Brings its Zoltan shield back online.

If any of your crew are on board when the Zoltan shield comes back on, they will be stuck and can't be teleported back until the shield is broken again (Doesn't matter if you have Zoltan Shield Bypass).

Dodge rateEdit

Assuming cockpit and engines are unharmed and the engines are fully powered. Based off system health of the engines and cockpit.

  • Base Dodge rate: 28%
  • If fully manned 38% (Enemy crew is unskilled regardless of difficulty)
  • If unmanned 22%

Note: This assumes the Flagship operates just like a player ship. Exploration using the editor suggest the ship automatically receives the fully manned bonus without crew. Granted, the player control Flagship had advantages the Boss Flagship did not have (Auto repair was on at all times while this only happens to the Boss Flagship if the entire crew is killed.)


Final boss4

The Big Bad Boss finally bites the inter-planetary dust.


Victory screen.


Victory Text

Finally, after the three toughest fights in the game the Rebel Flagship has been destroyed!

After this long struggle the victory screen appears. It has the name of your ship as well as the names of every crew member that survived the encounter. Note you can still win a victory even if your ship is destroyed in the process.

You will also have the words "Victory" if your ship is a new high score.

Recommended EquipmentEdit

FTL is less strict than most roguelikes, as far as the equipment required to beat the last boss goes. Still, when you get to the Rebel Flagship, you absolutely must do two things:

  • Not die, and minimize the risk of dying
  • Destroy the Flagship, rather than kill the crew, even if it takes a long time

These upgrades help you to fight the last boss while minimizing risk:

  • At least three layers of Shield.
  • At least level five Engines.
  • A way to damage the Flagship hull overwhelming, depowering, or bypassing its shields.
  • Maxed skills for men at stations.
  • At least six crew members.
  • Level 3 Doors to control fires and boarders
  • For the 2nd Stage, an attack method that does not rely on Missiles or Hacking to break through (due to enemy Defense Drone).
  • A way to quickly mow down Zoltan Shields of 3rd Stage (ion/beam weapons/drones, plain old big laser battery e t.c.) or Zoltan Bypass.
  • A counter to missiles: This is the key point, and can be done in many ways. Most of the Flagship's weapons can be endured with a strong shield and high evasion, except for the missiles. If they hit your shields, weapons, engine, or pilot systems, and you don't have redundancy, it may be necessary to jump out and repair.
    • Cloaking is a nearly perfect counter to missiles or super weapons to dodge them, and gives time to perform repairs so that you don't need redundant levels for damage buffer. However, it costs 150 scrap and the 20 second cooldown usually means you will be vulnerable every other volley: the missile system must be destroyed before the second salvo. Note that since you are dodging periodic attacks of short intensity, level 1 is all that is needed with good timing.
    • A Teleporter can slowly disable all the Flagship's weapons without needing ammo. By prioritizing the missile system you should only take a few hits. However, you won't be able to use the boarding crew for repair and defense on your own ship. Less effective in round three when the Zoltan Shield will block sending and retrieving crew.
    • Defense Drones to block missiles and Boarding Drones. If you don't have one or a couple combat specialists, the constant Boarding Drones will be huge trouble. Be aware Defense Drones can miss (expect at least one Boarding Drone to make it through), and cannot hit all three missiles the Flagship fires in a salvo. Two Defense Drones Mk I will be able to take down 80% of the boarding drones and almost every missile.
    • Redundant levels and a good repair crew: a Level 3 Pilot subsystem prevents a missile from knocking out all evasion. This is the least proactive strategy to cope with missiles, and it won't stop your hull from eventually collapsing.
    • For the first two stages, a Fire Bomb or better yet, a Breach Bomb are great ways to take out the missile launcher. The Fire Bomb will injure the gunner, cause a fire which may injure the gunner further, and the gunner will be too busy with the fire to man the launcher which slows down the launcher by up to 2 seconds. You will need multiple Fire Bombs to kill the gunner and destroy the missile launcher. The gunner can’t heal which makes all damage permanent. A Breach Bomb will destroy the missile launcher in one hit, heavily injure the gunner, and it will cause a breach. The gunner will need to seal the breach before fixing the missile launcher, which will buy time to get a second bomb ready that can finish off the gunner.
    • Hacking: Using this combined with Cloaking can effectively prevent the Flagship from ever landing a single missile volley in the first phase if you destroy it fast enough.  However be wary that the Defense Drone the Flagship deploys in its second phase can intercept the hacking drone (combining a drone launch with a barrage of weapon fire can increase its chances of getting through).  It should be noted that hacking the drone system will only disable the normal drones, not the ones that appear during a power surge.  Also be aware that the Super Shield in the Flagship's third phase can block hacking.  However if the shield is replenished once the drone is attached it will not stop you from initiating a hacking pulse.  Hacking the shield system will not destroy the Super Shield if it regenerates.
    • Mind Control: This can be a very effective strategy for neutralizing the Flagship's missile battery in all 3 phases as the room is sealed off (either have Zoltan Shield Bypass or a means of quickly taking down the Super Shield in the third phase if you plan on using this strategy).  Keep in mind that Level 2 or 3 Mind control also boosts the damage and health of the victim in addition to extending the duration of control, meaning that the missile battery can be more easily disabled with an advanced mind control system.


Some Augmentations are not as useful end game as others. Consider swapping out economic Augmentations, like Drone Recovery Arm, in Sector 6, 7 and 8 for more offensive/defensive Augmentations.

  • Shield Charge Booster: Effective in stage 2 for the near constant barrage of bombardment your ship takes.
  • Weapon Pre-Igniter: Basis for a couple of aggressive-kill strategies, plus all around good for instantly taking out some of Flagship's scariest stuff with missiles/bombs (which is the Triple Missile Launcher and other systems depending on your strategy).
  • Automated Re-Loader: Useful in nearly every playthrough as all your weapon systems will recharge faster.
  • Stealth Weapons: Allows much more flexibility in attacking the Flagship especially if you have level 3 cloaking.
  • Defense Scrambler: If you plan on Missiles or Hacking for Stage 2, you need this.
  • Zoltan Shield Bypass: Useful in stage 3 for boarding, mind control, and hacking.
  • Zoltan Shield, itself: A good enough reason to look towards more aggressive brute-force tactics like a Vulcan spin-up or shield takedown/beams fastkills. Coupled with cloak and dodge (remember, you could depower shields while Zoltan Shield still holds) this can often give you all the time you need.

The rest of the augments are mostly just a convenience and "I didn't find a better one" case. Honorable mentions go to Reconstructive Teleport and Hacking Stun as the amount of convenience they provide is so much it starts to spill over to just-inconvenience to the enemy.

It is important to have your augments synergize well with each other, your equipment, and your strategy for the Flagship fight. For typical fights, a balance works great such as having both an Automated Reloader and a Shield Charge Booster, but in the Flagship fight, 2 Shield Charge Boosters works better in most cases. The Weapon Pre-Igniter is great for typical fights, really helps to get to the Flagship, and even helps taking out the Zoltan Shield in the 3rd stage of the Flagship fight, but it is largely useless in the 1st and 2nd stages "played classic style". However, when the Weapon Pre-Igniter is paired with 1 or even 2 Breach Bomb Mark II's, Fire Bombs, or a combination, now you can delay (if gunner is still alive) or even take out the missile launcher at the beginning of the fight.

Defensive strategies are not the only option. Three Automated Reloaders are especially devastating in the 2nd and 3rd stage if they are paired with 3 or 4 Laser Burst Mark I/II's (L.B. M1= 3.96 seconds; L.B. M2 4.32 seconds to reload). It can even be helpful (though not without risk of prematurely ending the fight too soon) in the 1st stage by either taking out the missile launcher or the medbay quickly. A combination of Reloaders and Pre-Igniter coupled with Gatling and a small bit of other lasers will take down all 3 boss stages in seconds once you've survived the spin-up. Hacking Drone to Shields + Glaive and whatever other Beams you find + a couple of attacking Drones = oneshot Stage 1, oneshot Stage 2 with Defense Scrambler - else they shoot down hacking drone, - and two-shot Stage 3.

Possible strategies for easy difficultyEdit

Flawless Victory

With a good setup and strategy, it's possible to defeat the Flagship while taking no damage.

  • Mind Control and Teleporting the controlled Crewmember works for depopulating the Boss
  • If you are using the Federation Cruiser (note: the Federation Cruiser isn't unlocked until after you beat the boss), you will need to upgrade your artillery beam; at level 4 this beam is devastating as it ignores all shields and can be recharged quickly.
  • If you can somehow get 4 Burst Laser Mk II, you can easily defeat the flagship in about 10 minutes while taking minimal damage. Same miracle works with Chain Burst and Vulcan.
  • Pick up two laser weapons at least, as well as a missile/bomb based weapon, preferably Pegasus (two missiles can be useful in later stages). If you have decent boarding capabilities and a good defense, a working laser/beam is all you need weapons-wise. For speed the best would be Hull Smasher Laser II, Glaive Beam, Pike Beam, Chain Vulcan (though if you have this you really don't need boarders, or anything else for that matter), etc.
  • Make sure you have the maximum amount of crew that you can hold and you are ready to fight the final boss.
  • Don't delay in engaging the flagship; although there are some profitable encounters on the last map, taking too much time lowers the number of repair spots and time available to visit them. Since you have to fight three stages you can't wait until the last second.
  • IMPORTANT: Do NOT kill all of the crew members. If you do kill all of the crew an aggressive AI takes over and periodically repairs all of the systems that are damaged (similar to the Auto-Scouts). Who shall live depends on your strategy:
    • The basic and most ill-advised strategy is simply to kill all four gunners and destroy their weapons, then destroy the flagship with normal weaponry.
    • the "boarding" strategy is to leave the gunner of the triple laser (just to the left of the cockpit) alive, and kill the entire crew on the main deck before going to the next phase. This makes taking out the drone bay and shields practically a joke as your crew will go unchallenged into every room after the first stage. DO NOT attempt this without first destroying their (level 3) med bay unless using crystal crewmembers and their lockdown ability or the hacking system.
      • However, if you are relying on fire damage to win (not recommended) then you want to leave another crew member alive as this one cannot put out the fires, and repair damaged sections, which you will need repaired in order to deal more damage to the hull.
      • If this strategy fails (for any reason e.g. can't destroy the medbay, etc.), remember to kill the last gunner as you fall back to the basic strategy.
  • A good way to deal with med bay on the first stage, after you take care of people in isolated rooms manning guns, is to get your missile/bomb ready, teleport boarding crew in any room but medbay, fight till first bunch of Flagship's people run to medbay low-health, then missile/bomb/hack said medbay, not only damaging/taking it out, but also killing those unfortunate souls. Even if you then have to recall boarding party and remaining crew repairs medbay, repeated application of this tactics will kill off everyone in the main compartment possibly before the medbay is out.
  • IMPORTANT: If you do manage to kill the crew it does make the last stage of the boss much easier as you only need to worry about the super weapon. As for the aggressive AI, there are two ways to overcome the rapid repairs. One, use breach weapons. Like the AI ships, the flagship can't auto repair any system that has a breach in it. Two, it is easy to overcome at this stage with fire weapons as fire also disables AI repair, and fire also has a chance to spread causing further damage to the ship without having to deal with the shields. Though until their shields are down beam weapons, with the exception of the Federation Cruiser's artillery beam, are useless and with the crew dead you're free to target the shields with Bombs and Missiles.
  • In all three stages, the first thing to do is teleport two crewmen onto the Triple Leto Missile Launcher (the weapon directly to the right of the cockpit), the most dangerous weapon, as soon as you can. Then take out the triple ion weapon (unless you have level 4 shields and Defense Drone Mk. II, then wreck the beam). Only then do strategies diverge:
    • If using a full boarding strategy, destroy the beam weapon and leave the triple laser alone. It's time to assault the main deck.
    • Otherwise, take out the triple laser, then the beam weapon. Once you have taken down all of the weapons power down the teleporter as you won't be using it until the next round.
  • While your away teams are doing this you can start shooting for the shields; however, with a massive 4 points of shielding and a decent chance of dodging your attacks it is a tough nut to crack. If you have missile weapons you can easily bypass the shields and free up your laser weapons to tear it apart.
  • Once you have defeated it for the first time you should try and visit a repair station to heal your ship (assuming you actually took damage, which you really shouldn't have). If a repair station is unavailable, you can use a hull repair drone to fully heal. It doesn't even need to be active during combat; just swap it in after you've beaten a boss stage and use it at your leisure.
  • In the second round it is vital that you take out the weapons at the start again. Its super attack is a deadly swarm of drones that can tear apart any unshielded vessel in the 5-10 second period in which they remain on screen. However, with its weapons out of the picture, level 3 shields should be enough to survive. Level 8 shields plus a Defense Drone Mk. II make the threat almost non-existent. Before his weapons are down you can cloak to avoid the drone swarm - note that if you allow a L3 cloak to run its full length, it will recharge too slowly to avoid every wave. Decloak early, use Level 1 cloaking or take down the weapons (or, best of all, all three). Then you will have to take out either its shields or its drone control, as its Defense Drone will take out any missiles that you shoot in this round (except for the Pegasus's 2-missile firing system).
  • In the second stage, the first two priorities are destroying the triple missile launcher and drone control. The beam weapon comes third. In a boarding strategy, if you have a four-seat teleporter, you can do this by sending all four boarders to the missile launcher: Two of them will "overspill" into the piloting, and can reach the drone control unimpeded since the second stage ship has no door system.
  • Now that you have reached the final round, this is where things get tricky. It has a Zoltan Shield which absorbs 12 points of damage AND regenerates if the fight takes too long, so you will need to take it out before you can teleport in and take out the weapons. After the weapons have been taken care of you will need to take it out as quickly as possible; power down the teleporter and pour everything you have into the engines so that you can dodge the super attack. Alternatively, one can use a well-timed Level 1 cloak to dodge the super attack. This super attack shoots around eight lasers - this means that even if all of the weapons are offline you can still be hit by this. The Mind Control paired with the teleporter may even help you get more crew on board, as the Flagship may accidentally abduct your crew. Take out its shields as fast as possible then aim for the piloting. Then just shoot as fast as you can at whatever part of it, and it'll explode completely.
  • Congratulations! You have beaten the Rebel Flagship!

Boarding Strategy:

This strategy has been successfully used on most ships and elements of it should always be considered among the primary options. The core idea behind it is to use a relative safety of Stage 1 boss with missiles and EMPs disabled to set you up for much easier Stages 2 and 3, which normally could prove quite problematic and can not, unlike Stage 1, be "pacified" with a fast and limited effort.

To that end, at Stage 1 we are aiming at killing all Flagship personnel in main compartment, leaving only one dude in enclosed harmless weapon room (normally Lasers to the immediate left, Beam to the far right at Hard). This means some way of overcoming a high-level Medbay, either via Crystal Lockdown, hacking, or targeting it with missiles/bombs. Lasers can also work, but mean that you may need to commit an entire barrage towards disabling the medbay, leaving no projectiles to target other systems like cloaking, doors, missiles, etc.

Two general tactics could be employed: either taking out medbay first and then fighting crew coming there while preventing it from coming back online (such as with breaches, healing bombs for your boarders, hacking, fires, etc), or boarding at a different room and timing your missile/bomb/hacking efforts in such a manner as to kill low-health enemies the moment they enter a medbay (or, for true micro/timing mages, en route there).

Most of the time you will need repeated "go"s to finish everyone off. Care should be taken as to not deplete boss's hull before this is accomplished.

Third variant to the same end could be called the reverse boarding technique and borders on mechanics-abuse. Mind-controlled enemy crew counts as your own for the purpose of Crew Teleporters. Therefore mind-control, teleport back to your ship, and wait for it wear off while following him around with a "quarantine team." Abduct, quarantine, rinse, repeat until all desired enemy personnel are dispatched.

Useful equipment, system levels, and personnel:

  • Good boarding team, at minimum 2 green skill, as ideal 4 gold skill. Mantis, Rock, and Crystal are the best so try to pick up these crewmembers whenever possible.
  • Level 2 or 3 teleporter.The large one isn't required, but if yours is small you definitely need it to be level 3 (or you need the healing bomb or Rock/Crystal boarders or Clone Bay).
  • Level 4 or 6 shields. Level 6 is safer, but level 4 is manageable with a high-level engine and a defense drone mark 2.
  • Level 6+ engines.  More is better.
  • Level 2 or 3 cloak.  The super weapons the boss has fire off about every 25 seconds or so, so level 2 or level 3 cloak won't allow you to recloak in time, but you still need a damage buffer so you can keep cloak online if it gets damaged.
  • Defense Drone, preferably mark 2, though mark 1 also works well (if you have 3+ shield layers you might actually WANT mark 1 so that it isn't distracted by lasers if by chance laser shits and a missile come at once).  With 4 boarders I also really like the system repair drone.
  • Breach bombs, Pegasus Missiles, or Breach missiles. Or Hacking. Or Crystal Lockdown (on a dude or on a bomb).
  • Any sort of laser or beam weapon (the power of the weapon doesn't matter here, except to make fights shorter).
  • Level 2 or 3 doors.
  • Level 2 clonebay. It is you best way to deal with neverending brigades of boarders in your ship.
  • Mind control: If combined with cloak and upgraded this can allow the mind-controlled missile gunner to destroy the system even before it can fire off a volley.  Also good for giving you reinforcements aboard the Flagship when you board and good for covering your own ship in the third phase when the teleporter is used (a Level 2 Mind control system will ensure an enemy boarding party is severely undermined as your mind-controlled crewman will prevail as a result of the damage and health boost though this is not significant enough to leave him/her with much health). A Level 3-mind-controlled victim will have a larger amount of health once the control wears off and thus it is not recommended to use it, unless you have him in the full medbay and intend for him to die, in which case the extended duration makes up for the extra health and is the only way to ensure death.
  • Level 2 or 3 Hacking: Excellent substitute for Crystalline Beings or Lockdown Bombs. Put this guy on the Medbay, power it down, board the medbay, then as soon as it's full just turn it back on. The crew inside dies from the joint power of the hacked medbay and your boarding crew, which then has a chance to destroy the medbay, allowing them to do their job as normal. Excellent with four-person teleporter.
  • Provided you necessarily need Teleporter and auxiliary systems are limited to the total of 3, you will want at least 1 of remaining 2 to be of "defensive" nature (Drone bay and/or Cloak). Setup of Teleporter-Hacking-Mind Control is the most problematic because of it's extreme vulnerability both to whatever volleys of missiles Flagship will send each stage before missile launcher is neutralized and to stage 3's "taking fire while working on Zoltan shield". This could be worked around with stuff like weapon pre-igniter (pre-igniting missiles to missile launcher) and Zoltan bypass, but you are far from guaranteed to ever see those.
  • Which means, yes, ships with Hacking and Mind Control as their starting systems are naturally unfit for the boarding boss tactics.

Round 1:

  • Start by turning your defenses up to maximum.  At the moment, you don't need any more offensive power than your teleporter, so turn your weapons off if it means having level 6 shields and near-maxed engines.  A defense drone is nice here, but isn't required yet.
  • Teleport 2 of your boarders into the missile launcher room (just to the right of the cockpit).  Don't retrieve them until they destroy the weapon.
  • As soon as your teleporter is off cooldown, send your other boarders into the ion weapon room. Forget this step if you have level 8 shields.
  • When possible, retrieve your original boarders and then send them into the beam room.
  • When those three weapons are dead, the only attack the boss has is the triple laser.  If you have a level 3 shield, feel free to reroute power from your engines to your weapon systems.
  • After your boarders have been healed in your medbay, use your missiles or bombs to destroy the boss' medbay.  (If you used breach weapons, wait until they fix the breach before continuing). An even better strategy is to hack the medbay while it's intact, then board it with hacking off, then as soon as it's full turn hacking on and start a hacking pulse. This eliminates any chance of missing, reduces damage to your boarders by distracting enemy crew with breaking out of the medbay, and eliminates the missile cost.
  • Heal Burst is quite useful here.
  • Get all of your boarders into their medbay as fast as possible.  You should be able to kill nearly all of their crew before being forced to retreat since they won't be able to heal themselves.  If you need to pull your boarders out, repeat the last two steps until only the gunner to the left of the cockpit is alive.
  • Have your boarders take out the shield generator and piloting then pull them out. If some boarders are not gold-level yet, you can train them on the various systems. Just remember not to destroy the Oxygen, and if you used missiles against the medbay remember that destroying a system takes out one of the ship's hull points: You don't want to accidentally destroy the ship with your boarding crew.
  • Use whatever weapons you like to destroy the helpless boss.  It is mildly amusing to destroy it with a weapon only poor transport ships use (the dual lasers), or even better, the basic laser. Hull Laser Mk. II does an excellent job at dispatching it fast, as does the Glaive Beam.

Round 2:

  • Switch back to your defensive setup, but make sure that you have a defense drone on.  You really don't want to have your non-combat crew having to deal with boarding drones here.
  • Remember to use your cloak when you see the power surge warning.  The extra six drones are the scariest thing the boss has, but fortunately it lasts for only five seconds.
  • Teleport 2 of your boarders into the missile room again and take it out.
  • When your teleporter has recharged, send your other two boarders into the drone control room and destroy it.  This will stop the annoying boarding drones, the defense drone, and the normal anti-ship and beam drones the boss uses.  Turn off the defense drone, and use that power to activate your weapons.
    • If you have a four-seat teleporter, you can do both at once by sending all four boarders to the missile launcher: Two of them will "overspill" into the piloting, and can reach the drone control unimpeded since the second stage ship has no door system.
  • Once the missiles have been destroyed, have those two boarders switch to the beam weapon room.  Once that is destroyed, have them join the second group of boarders in the main section of the ship.
  • Once the drone control is destroyed, take out the shields and piloting. Then retrieve your boarding crew.
  • Kill the boss again with whatever weapons you see fit.

Round 3:

  • Switch back to defense mode.  Note that you do need at least 1 weapon active here, or the Zoltan Shield Bypass.  Don't forget to activate your cloak to avoid the super weapon shots.  (Can also get you an achievement in the stealth cruiser).
  • Take out the Zoltan shield. Ion/Beam weaponry is recommended. If you have Zoltan Shield Bypass, just beam your guys in and laugh at the idea that they could possibly be stopped.
  • Send 2 of your boarders to destroy the missiles (again).
  • Send the other 2 to take out the shields.  You may need to take out the Zoltan shield another time or two.
  • Once the normal shields and piloting are down, retrieve your crew and destroy the boss (again) with your amazingly powerful dual lasers and/or leto missile launcher. If you can set the flagship on fire, do so, and kill the laser guy, so the autorepair starts and the fire does constant hull damage. And you can get the "Some people just like to watch ships burn" achievement.

The hardest part is taking out the crew in round 1 (unless you have hacking, in which case it's laughably easy and you might actually laugh at the pathetic little humans trying to run away from their inevitable demise).  After that it's a pretty easy fight as long as you leave the near-useless laser gunner alive.

Possible strategies for normal difficultyEdit

  • All plans require a lot of scrap, and the higher the difficulty, the less you get.
  • Therefore you should really start paying attention at less conventional "fast-kill" strategies, which are way more specific in configuration and might take serious bit of shopping around, BUT which easily save you 400+ scrap in shields and engines not needed because you don't plan to stay and "withstand boss fire", you plan to stealth-dodge a couple, Zoltan a couple, soak up a small couple, even, but destroy the flagship before taking too much damage. Honestly, you see a Vulcan? Grab it if at all possible! And suddenly you don't have to worry about "battle with a boss", you only have to worry about "how to sustain 4 health levels in my weapon system + 2 more or 2 in attacking drone system for a small bit of support for 50 seconds under boss fire". Bring DNA storage and hull repair drone, and you could afford it on 1-hp-hull, all-other-systems-red, fully vented all crew dead ship!
  • Bear in mind that if you strategy requires a certain realistic amount of luck (like 50%), you can jump away from the Flagship, repair and go again.
  • The fundamental difference between a legitimate "aggro" boss strategy and just a noob poking hopelessly at Flagship is respect. Respect for 4 points of shield coupled with high evasion and a full room of specially trained monkeys to repair it in case of emergency, respect for hitting power of triple weapon batteries and beam on weak-shielded, etc. "I will likely take one beam hit to the hull before he is gone, and if it doesn't hit weapon system I win" is realistic chances and proficient Hard planning. "I will just aim a Vulcan at it and hope it dies first" is not (hint: without other specific efforts, most likely you will).
  • Some of the fast-kill strats and "suicide survival" ideas are already mentioned. Other, you are free to discover, explore and add!
  • During the first stage of the boss fight, your main priority are the weapons, since they cannot be repaired if you kill the crew manning them (unless you kill off all of the crew/ship teleports away). Go for the triple missile launcher first if you don't have any defense drones, otherwise take out the triple ion blast. If you're not doing damage fast enough, then it might be a good idea to focus fire their shields first. Low damage or shield penetration will prevent you from damaging the flagship's weapons fast enough to protect you. If you have missiles/bombs, use those to take out the shields, then use your lasers to take out the weapons.
  • During the second stage, it loses cloaking and ion blast, but starts using drones. It also has a special move telegraphed by the "power surge detected", which releases many more laser and beam drones. Disabling the drone control will not nullify the power surge, but will deactivate any other drones, particularly useful when the flagship has a defense drone. The Flagship will also release boarding drones. They will harass your crew non-stop, since you can't "guide" them to your medbay by opening all the doors except some. (Note: The Boss's drone system has a power queue just like yours, if the boarding drone annoys you, just do 1 point of damage to the drones system and the drone will power down for the duration of the battle, or until the monkeys with wrenches the rebels call crew patch it together. The defense drones are last in the cue, so only a boarding crew can reliably shut down the defense drones.) However, after a large number of defense drones, the flagship will eventually stop launching them. A defense drone of your own can quickly cut through those reserves. You want to target either the triple missile launcher or the drone system.
  • Finally, the third stage, and the easiest if you have good shields and evasion. The Flagship starts off with an enhanced Zoltan Shield, taking more hits than a regular super shield would. In addition, the power surge shoots  many lasers at once, OR fully recharges the super shield. It only has a triple laser, and a triple missile launcher as weapons. This is a problem unless you have a weapon pre-ingniter because he can get a few shots off before you even take down the super shield, and possibly get a power surge off before you do any real damage. If you have 50% evasion and three layers of shields, the power surge should do little to no damage. The flagship will also start using its teleporter. Thankfully, they can be "guided" to your medbay, and humans are only average in combat. Focus fire their shields or their weapons.
  • Congratulations! If you have beaten the Flagship then give yourself a pat on the back, because Normal difficulty doesn't mess around. These tips are just guidelines, because situations will vary depending on the circumstances. Adaptability is key.

Circumstances on hard difficultyEdit

  • Now the Laser and missile system is connected to the main body of the Rebel flagship. This is critical to a lot of boarding strategies and overall strategies which concentrate on disable the missile system. Now the crew can heal up and even repair those systems, which isn't possible in the easy and normal difficulties.
  • Actually the fact that the rooms are connected might present you with more advantage. If you are able to kill enemy crew members via certain means, such as crystal lockdown, you can just keep one enemy alive while your borders remain on the ship wrecking havoc. Keep the enemy medbay intact and then the enemy will continuously heal in the medbay, preventing the flagship from going into auto mode.
  • The 1st and 2nd phase is more or less easy, if you are able to knock out the Rebel flagship quickly enough, but the 3rd stage is now a lot harder, as you have to deal with more boarders (2 from the weapon systems) and repairable weapon systems, as you get boarded.
  • A very skilled and balanced crew is very vital!
  • Or it isn't. One way to survive Stage 3's avalanche of boarders is to just vent the ship aggressively, relying on Clone Bay to keep crew in existence, running around distracting boarders being the last miserable thing their original bodies do (unless we're talking Lanius ofc, in which case it's all just business as usual). You can win without manned bonuses on your stuff; you cannot with your ship overrun with boarders.

Exploring the Flagship via FTL EditorEdit

Using the ComaToes Profile/SavedGame Editor (AKA FTL Editor v15), it is possible to look at the Flagship(s), its weapons, and its drones. It’s even possible to play as the Flagship(s). The information gleaned with the editor is likely not 100% accurate as a player control ship is not 100% like the boss encounters. The editor is still the best source presently available.

There are 3 models for the Flagship corresponding to the 3 stages. The hull strength varies slightly (20 in the 1st and 3rd stage/model and 22 in the 2nd stage/model). Unlike the boss encounter, when the hull of the 1st or 2nd model is depleted, your ship is destroyed and you see the game over message. Reactor power varies greatly but is always higher than a player can get without Zoltan or cheating; 1st=42, 2nd=44, and 3rd=31. What’s odd about these power amounts is the Boss would have leftover power even with all systems fully charged. The 1st stage could only be charged up to 31 (11 leftover), 2nd stage 35 (9 leftover), and final stage 29 (2 leftover). This assumes the Flagships weapons operate like Special Weapons. Even if you assume the power surge special abilities use actual power, that wouldn't explain the first stage that has no power surge. The power surge special abilities are unavailable to the player.

Playing as the Flagship also showed some odd things. Unlike the boss encounters, the Flagship's auto repair is turned on even when you still have crew. I had a crew member repairing a badly damaged system along with the auto repair. The crewmember sometimes did not receive repair EXP because of the auto repair system got the finishing repair. I did not need a crew member in the cockpit (or even on the ship) for an FTL jump, and I also still received a manned bonus for both the cockpit and the engines even when no one was there. If those positions were manned, the crew member received experience and upon the first level up, I would get for example that extra 2% to evade. I presume this is true for shields as well. Just to be clear, I could fly the ship without any crew. If my crew died, the game kept going so long as the ship was still flying. While flying my empty ship, I encountered a ship which demanded I give them a slave, I picked the "Draw Straws" option and the slavers flew away. While playing as the Flagship, you are still limited to 8 crew. While in the editor, I accidentally gave myself 9 crew. When I started the game, I was immediately prompted to dismiss one.

When you play as the Flagship, the ship's layout converts to the player's ship layout. In the editor, no work station is visible, but when you play the game as the Flagship, the work stations and other doodads appear. Most are unremarkable with 2 exceptions. One, the 4-person medbay becomes a 3 person medbay with the bed doodad appearing. Two, the four manned weapon stations don't appear. In the player menu, the weapon section and drone control are literally on top of each other.

The first 2 stages have 4 drone slots while the third stage has none. When playing as the later stages of the Flagship, you can try to buy replacement systems for the systems you don't have but they won't appear. This includes Weapon Control.

Finally when playing as the Flagship, you do not have the Flagship weapons. Instead, you have the Federation Cruiser special weapon. You might technically have 2 or even 4 of these, but the game interface doesn't let you put power in the other special weapons. There is only one Special Weapon spot on the player's menu (both upgrade menu and normal gameplay). I might have done it by allocating power in the editor but I am not certain and it was a fight to allocate any power in the editor.

You can get a version of the Flagship weapons by giving them to non-Flagship ships via the editor. All the weapons required only 1 point of power and have graphics corresponding to the weapons the Flagship uses. The missile launcher didn't consume any missiles. There was two version of the triple burst laser. The only performance difference was one had a 16 second cool down while the other had 20 second. The other weapons all had 20+ seconds cool down with the longest belonging to the Ion weapon. It should be noted the game files also had a normal weapon version of the Federation Cruiser special weapon. This version took 40 seconds, which corresponds to a level 2 version of the special weapon, not level 1. It is possible the normal versions of the Flagship weapons are also the equivalent of a level 2. For more information, look at the Weapon page. The weapons are not in the table sections but they are in the list sections.

Finally, the Flagship also has a special variant on Boarding Drones (and the Defense Mark II drone, which is unused). The key difference is they only use 2 power instead of the 3 the normal versions do. For more information, look at the Drones page. The Drones are not in the table section but they are in the list section.

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