What information could be so important that it could save the near dead Galactic Federation? What information could be so special that it couldn't be transmitted? What information was so unique that you couldn’t switch ships? What information is so valuable that pirates would be sent after you for information they needed to steal? What information could be so worrisome for the rebels that numerous rebel fleets were sent after you? What information would be so powerful that the Galactic Federation would send you alone against the Flagship and not a score of Galactic Federation Carriers or Cruisers?
Being something of a tec geek, it could only be ECM, ECCM, or both. What is ECM and ECCM? Electronic countermeasures and Electronic counter-countermeasures (Europeans call it, electronic protective measures [EPM]) are both parts of electronic warfare. Both of these are real technologies that aircraft, subs, and navy ships use in modern warfare. ECM tricks things like sonar, radar, or other electronic detection methods. It can make it impossible for a missile or other type of weapon to lock on. Stealth technology is ECM. One form of ECM is having aircraft shaped in a manner that confuses radar. Jamming radar, radio, etc are also examples of ECM. ECCM is the counter such as building computers that can make sense of a confused radar contact. Both ECM and ECCM use numerous technologies to fight each other. (If you want more info, I included wiki links at the end of this blog.)
Getting back to the game, your ship could have either ECM or ECCM. Consider electronic countermeasures (ECM), it could hinder the flagship from targeting your ship. Not considering the Rebel Flagship special attack abilities, the ship’s weapons aren’t really that impressive. The ion laser takes 28 seconds to charge to do at most 3 ion damage. Every other ion weapon (6 out of 7) with the exception of the Ion Stunner can do the same amount or more ion damage in a shorter or equal time. Both versions of the Boss Laser only do 3 points of damage at most but takes 16 or 20 seconds to charge. Most lasers could out DPS this laser. The Boss Missile is about equal to the Swarm Missile, but the Swarm takes 2 seconds less and is more flexible when you fire it. The Boss Missile doesn’t consume missiles but the swarm virtually doesn’t with the right augment. The only weapon that’s somewhat impressive is the Big Beam. It is 25% longer than the Halberd Beam, and does the same damage, but it takes 26 seconds to charge. The only redeeming feature of the boss weapons is they all take 1 point of power, but they have charge time of on average 23-24 seconds (After the wiki links, you can find a quick list of boss weapons charge time and damage amount). Given the size of the weapons, you would expect them to have more firepower. However, these weapons would be very effective if there cooldown reduced by half, or their damage doubled, or shot twice the number of projectiles.
ECM could be harming the Flagship’s weapon systems by a few ways. The Flagship fight would be almost impossible if the weapons had only a third of the cooldown, or did triple the damage, or shot thrice as many projectiles. The player ship could have ECM that forces the flagship weapons to take much longer to charge. Another way, the Rebel Flagship’s weapons were built more for planetary assault hence why it is game over if the ship spends 3 turns at the Home Base. What if the player’s ship had ECM that messed up the anti-planet weapons and the Flagship used either lesser setting or secondary weapons. This would explain the lack of fire power on the Flagship. Either way, the Flagship would slaughter any escorts. It would also interest pirates because it could be sold to interested buyers.
The Flagship could have next generation ECM that radically increases its evasion rate. It always seemed odd that the ship only had level 2 engines. However, if the ship had special ECM which made weapons lock very difficult and thus made its evasion rate four times higher, 80%, the Flagship would be almost invincible. If the ECM made evasion rate 5 times higher, 100%, only boarders and the Artillery beam could harm it. The only way to counter such a system is with an effective ECCM. Maybe the Flagship weapons are lacking because only 1-power weapons would work effectively with the Flagship super ECM. This would explain why the player ship doesn’t enjoy any special advantage against other ships. It would half explain why you have no escorts. Only half because you could destroy the Flagship engines and then the other ships could open fire. So why doesn’t that happen?
My best guess is the player ship has a special combination of both systems that exploit weaknesses in the special weapons and other systems of the flagship. Part of the player ECM could include the hull, which would mean you can’t succeed in another ship. If other Federation ships can neither target the Flagship nor survive a volley from the Flagship, then escorts would be utterly wasteful.
Boss Weapon Stats:
Heavy Ion (Boss): 28 seconds, and 3 shots 1 ion damage
Boss Laser: 20 seconds, and 3 heavy laser shots, 1 point
Heavy Laser Mark 1 (Boss): 16 seconds, and 3 heavy laser shots, 1 point
Boss Missile: 23 seconds, 3 missiles 1 point
Boss Beam: 26 seconds and 2-piont beam