Right, bit of backstory behind this, its a good story:
So I'd just completed the molecular relay quest with the minutemen, and all was going well. In the playthrough im doing, im rocking a stealth build. Deliverer pistol with a load of ammo, and a ghillie suit from a mod (jump to lvl 120 too). All is going well, and i arrive in the institute. I talk to father, i answer all bad things, until he asks me to join with which i say "Maybe" and that goes on. So being the perk filled level 120 that i am, i decided to kill everyone in the institute one by one. I clear the top tunnels, bam. They see a dead body and they move on. They see their friends die right in front of their faces and they carry on. Did this for a while, but around halfway through it gets really strange because there was a guy talking to a synth, i shot him mid-dialogue, and he kept talking. I cleared the whole place and got in the elevator to the top floor. I walked past the room and to the relay hall and, OH GOD. Around 50 synth exterminators (i think thats what theyre called, the highest level ones). I manage to kill half of them (stealthly with my pistol, but i walked up to them before and they didnt attack me, killed the ones left side of first photo) , i walk over to them to check their loot, and the right side becomes hostile. I RUN to the elevator (forgot to put network scanner in and theres no way im getting in that terminal) and im free. I'm safe in the elevator. I make it to the bottom floor and boom, second picture (end of the corridor, LOADS of em). I walk over to em, they become hostile, but not before i see that between me and the elevator, the room was square formation packed with synths. I'm panicking. I'm scared. I'm gonna have to reload a save from ages ago. I manage to dart through the remaining synths on the top floor and to the terminal just about, plop the scanner in and leave, 30 stims, and about 1000 bullets lighter. This would break my mind if i was on vanilla, but i don't even know if it was the stealth killing or the mods.
Mods i had installed:
Cheat Terminal (for pistol, ammo, little jump boost, and lvl 120)
Greens Ghillies (for ghillie armour, but i dont think that would do anything to the institute. I mean, why would it?)
Snow Graphics Mod (for visuals, don't see how it could affect anything in the institute)
TL;DR: I stealth kill everyone in the institute and get trapped by 100+ synths.
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