Hmmm. I won the battle (expedition) but lost the war (freighter base)… The spreading blue cubes are closing in on me… 
(Aside: By default "others can build in my base is enabled, but I switched it off half way through this expedition.)
I might have a quest for all you all… How do I remove this evil room?
If I stand close to it I can open the build menu and press X. Then it says “deleted” (it always says that, independent of reality) and then “player is inside” and then it does a whole lot of nothing. Same if I try to replace it with an open-walled cargo room, or if I try to place a door on it, nuthin. I also tried standing one floor above it on the balcony, and I tried pressing B to move the camera, but can’t leave the room.
What else can I try, other than resetting the freighter?
Now that the expedition is over (and singleplayer) I should perhaps move house and commandeer a new freighter. I wonder whether the curse will be transfered as well.
PS: I checked out some NPC freighters (which can now be bought by just asking the captain?) and … I think their subtlety generators were offline. “It’s not mine officer, I swear! It was… procedurally generated, I swear!” 
