Fallout 4 created by Bethesda Game Studios.
Images used for educational purposes only.

Prerequisites: Complete The Molecular Level, and possibly Institutionalized
Trigger: Special; see below
Reward: 300 XP

So here’s the thing. Not everyone likes the Institute. In fact, there’s a pretty solid chance you don’t like the Institute, which means you don’t want to side with them in the war at the end of Fallout 4. Unfortunately, Father isn’t too keen on just letting you leave without a really good explanation. That’s where Banished from the Institute comes in.

Banished from the Institute is a special quest that you’ll only get when you do something that really pisses off the members of the Institute. Usually it entails somehow betraying them to one of the other factions, but there are other ways to get it as well. Regardless of how you go about triggering Banished from the Institute, you’ll be immediate barred from ever returning to the underground facility via your Pip-Boy, and the Institute will once again be hostile to all of your efforts. Keep that in mind before you peeve ‘em off.

There are multiple ways to trigger Banished from the Institute, falling into two broad categories.

Kill People

Yep, simple as that. If you murder the right people in the Institute the members of the faction will become hostile to you, and you’ll be forced to escape by fleeing to the teleportation pad where you appeared in the first place. The difficulty of doing this changes depending on whom you kill:
  • Father. If you decide to kill Father (brutal) you will instantly be branded a traitor, and on your way out someone will yell at you through a loudspeaker to make you feel bad. This is by far the easiest way to trigger Banished from the Institute, as he’s standing right by the elevator you need to use to escape.
  • The Institute heads. Kill two or three of these guys (Ayo, Holdren, Li, and / or Filmore) and the Institute won’t be happy. Emotionally it’s an easier route to take, but practically it's difficult, as you won't be right by the elevator. You may want to wait until you get pulled into a meeting with several of them in the same room, which happens a few times.
  • Scientists. If you go on a murdering spree and kill enough scientists (the Institute doesn’t seem to care too much if you destroy Synths) you’ll trigger the quest. This is probably the hardest way to do it, as the Institute is filled to the brim with murderous bastards - and they can often shoot through walls, for some reason. Cheap! Stay near Father’s office during your assault.
Regardless of how you do it, return to the teleportation pad and hit the emergency button on the first computer console you see. This will activate the teleporter and allow you to escape.

Help Other Factions

None of the other factions like the Institute, not even the Minutemen, and there are several opportunities to betray the Institute while performing outside missions. The missions are as follows:
  • The Battle of Bunker Hill. At the beginning of this quest you can alert both the Brotherhood of Steel and the Railroad to the operation, and they'll give you different objectives. If you do anything other than reset the Synths (namely, kill or release them) Father will be peeved, and admitting that you screwed the Institute over without apologizing will get you kicked out.
  • Pinned. This short quest probably has you facing off against the Minutemen while trying to nab a scientist for the Institute. If you order the Minutemen to attack the Institute and then assist the soldiers in taking down your Synth contacts you'll be declared an enemy and kicked out of the Institute.
  • Spoils of War. This quest for the Brotherhood of Steel will force you to choose between helping the Brotherhood nab a piece of valuable equipment from the Mass Fusion Building, or aiding the Institute in the exact same manner. Choosing the Brotherhood will trigger Banished from the Institute, and you'll resolve the quest when you enter the Institute upon completion of Ad Victoriam.
(I'm sure there are more. Still working on this section.)