Fallout 4 gets weirder

[MazdaGamer]

Okay i have mods but none of them are supposed to do this. Idk if its the mod or the game is bugged but take a look:
Im invading the institute and a synth is friendly, the brotherhood doesnt attack him, its weird:

 

[Jassassino]

Prior to this you can hack a random terminal in father's room (I believe) which has commands to make the final battle easier by turning some Synths into friendly. These are accessible prior to the final battle. You may have accidentally activated one of these.

Terminal doesn't really explain what you're doing when you click on it but that's what you can expect from a game which has no cohesive direction like Fallout 4 unfortunately.

 

[Big No]

Considering how buggy Bethesda games can potentially be, this is the least of your problems.