Shooting Father and the 4 department heads is one way to start the Minuteman ending. Killing people in the institute would lock you out of the institute and railroad endings. What happens if you kill everyone in the institute? One bonus of meeting her is that she’ll modify your Pip-Boy with the ability to fast travel in and out of the Institute.
After that eject it back out and you’ll be able to fast travel out…at least that’s what it was for me. Make sure you load your “Network Scanner” holotape in a terminal inside the institute. Once you are in good graces with him, he will allow you access in and out of the Institute. You need to complete the quest that Father gives you. Talk to her and try to convince her to come back to the Brotherhood of Steel.
Enter inside and find Doctor Li in the room on the right. Head into the main square of the Institute, then follow the path to the Advanced Systems division. Once you’ve gotten inside the Institute, you’ll have access to reach Doctor Li.
