What about having the core progressively go towards more efficiency, for example asking to replace the defensive fleet with something of his own choice...then giving the player various quests, like the retrieval of other cores, or funds or whatever, so it can build some extra infrastructure...then you have the core rolling out redacted ships mixed with regular ones, eventually deciding that for the good of the colony, using only redacted ships is the better choice...
Basically the core can progressively make more and more demands until the colony becomes so strong that they deem you unnecessary, at that point there could be a huge fight where you defeat the core, and you can either remove it, or keep it as is, because it now understands that staying at peace with you is the more sensible choice. At this point you could get a say in some of the choices like what ships to use, or leave him be, you'll get to keep some of the cool stuff but after the fight the colony will be in a pretty sorry state, possibly permanently in some areas. All in all, you'd have to decide for yourself if it's worth it or not