How am I supposed to finish the game? I’m hostile with BoS and the network scanner is on the Prydwen…

If you are just looking at the quest marker, go and actually look. If you turned in the scanner to her for Outside the Wire, she was down at the airport and the game should keep her there somewhere near Prime for the rest of the game. There shouldn't be any condition that moves her back onboard the Prydwen specifically because of the network scanner. The game is set up to never remove the Minutemen ending, even if you try very hard to break quests.

If she isn't near the scaffolding or inside the room with the disassembled Prime, then you get to learn how to climb the control tower and see if the quest marker is right. It's not hard to get up there.

/r/fo4 Thread