On Hard mode, two additional rooms link the Laser and Missile ones to the main section of the ship. 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). The Rebel Flagship limits Sensors functionality capping them at level 2: enemy system power use or weapon charge progress are only available through hacking. If you have a clone bay, any of your crew on board the Flagship can be cloned after it jumps away, unlike any other battles in the game. There is also a slight chance for a random weapon or augment being dropped.
These rooms are also isolated from the main structure of the ship (with an exception on hard mode).Īlthough the Flagship uses a missile launcher, it does not consume any missiles and will therefore never run out of ammunition.Īfter the Flagship jumps away, the player will receive a small amount of scrap, fuel, drone parts, and/or missiles. They cannot be manned, despite containing crew. The Flagship's "weapons" are artillery systems, each located in its own room. The Flagship will then behave like an automated ship: undamaged systems are treated as manned (even those that are hacked), and damaged systems are all progressively repaired at a set rate, except those with fire or a breach in their room. Instead, a message will state that the AI took control of the ship. Unlike other battles, killing the entire enemy crew won't defeat the Flagship. If the player jumps away from the Flagship before completing a stage, the same applies, with one exception: the crew is fully replaced if the player retreats during the first stage. Only the crew is persistent through each stage crew members killed are not replaced on the next stage. Hull and system damage of the Rebel Flagship will be repaired on the next stage. 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. This happens again when you destroy the second stage, but not after destroying the third stage. When you destroy the first stage, you receive a high scrap reward at sector 1 value. Other systems will be installed on the next stage, changing its behavior dramatically. 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.
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