Cloaking causes the opponents weapons to stop charging and their anti-ship drones will drift, re-targeting when cloak finishes. This means that it is usually best to activate cloak immediately after the enemy fires their weapons; this will cause the shot to almost certainly miss, and then drastically delay their next shot. This can effectively grant a 2-volley advantage over the enemy. Beam weapons are less vulnerable to this, as the AI will likely fire the beam just as it is fully locked-on, and a fired beam will not miss even if already cloaked. However, cloaking before a beam is fired may be helpful if shields are down enough to where the beam would hit the ship, thus giving them a chance to regenerate.
Firing weapons while cloaked will shorten the amount of time the ship can stay cloaked. The Stealth Weapons augmentation negates this penalty.
After coming out of cloak, the system takes 4 Ion Damage as a cooldown. Note that maintaining cloak for longer increases the effective time between cloaking activations, as the cooldown does not begin until cloak is deactivated. Although all conventional enemy weapons cannot charge up during cloak (including the Rebel Flagship's four artillery bays), one notable exception is the Rebel Flagship's Power Surge in its second and third forms, which fires on a timer independent of targeting. As such, when fighting these forms, one should either keep the Cloak system on a lower power level so that it is available during each volley, or fire a weapon immediately after Power Surge ends to decloak and begin the cloak cooldown.