The most satisfying way to beat the flagship IMO is to first kill it´s crew (by whatever means. I like to kill them one by one by locking them in a room with a lock bomb and teleporting in) and then set the ship on fire (fire bomb or firebeam). With nobody to fight the fires, you should have an enjoyable time watching it burn
It helps if you have drone systems and hull repair drone to repair your hull points after the flagship jumps away.
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