What happens with Dr. Madison Li after the destruction of the Institute with all three remaining factions still alive?

She gets upset if Liberty Prime is used, but in that outcome, it isn't.....

Depends on if you got her to work with the Brotherhood again or if you activated the Evacuation Alert for the Institute. If not, then she is dead. If you activated the Evacuation Alert, then she might have gotten out, but there is no way to be sure.

Making Madison Li unhappy is major goal of mine. I can't stand her.

She hates it if you convince her to work for the BoS, she feels betrayed. Death is instantaneous, living a miserable life and work for a group she feels betrayed by, priceless.

Madison Li at Institute: "Don't act like you are important enough to know why they want me, you Brotherhood thug!"


Madison Li at Prydwen: "Why didn't you tell me it was Liberty Prime! I refuse to work!"


Though this does let you deliver one my favorite sarcastic lines in the whole game in a smug voice: "Someone's a liar! And it's not me!"

Nah, I convinced her to rejoin so she would have a front row seat to the fireworks display I'm throwing for the BOS shortly. I'm so considerate

Looking forward to finding this out. I rebuilt Prime, but am using the MM to take down The Institute.