The Institute is usually the last faction you will meet in Fallout 4. Until you meet them personally, you will only find out tidbits of information and hear the fears of them from others in the Commonwealth. (There will be massive spoilers for the Institute in this guide). The Institute headquarters is located under the ruins of the Commonwealth Institute of Technology, or CIT. It was largely founded by scientists from the CIT who survived the war. They aimed to continue advancing technology to help rebuild the Commonwealth.
They initially intended to work with everyone else in the Commonwealth. However, there were fears about their true intentions, and people were afraid of the synths that they were building. While the Institute’s vision was positive, they were willing to use any means necessary to achieve their vision. Fears of the Institute were vindicated when the Institute sent a synth to ambush a meeting between the various Commonwealth groups, and they have essentially been enemies since.
The Institute are directly tied to the Lone Wanderer, as they kidnapped their son from Vault 111 while the inhabitants were kept in cryogenic states. They used Shaun’s DNA to perfect the human side of the synths. Shaun was useful because he had been preserved since before the war, therefore his DNA had not been exposed to radiation. The Gen 1 and Gen 2 synths were easy to identify as synths, but the Gen 3 synths created using Shaun’s DNA were indistinguishable from humans.
Virtually everyone in the Commonwealth has problems with the Institute. Those afraid of synths believe the Institute’s creations are dooming what’s left of humanity. Those who believe in synth rights, like The Railroad, are opposed to the Institute due to their enslavement of synths. The Institute’s general practices often cause harm to the people of the Commonwealth.
How to Find and Join the Institute
You will likely hear of the mysterious Institute as you interact with others in the Commonwealth. As you progress through the main story and the questlines of other factions, you will eventually get to the quest “The Molecular Level”. In this quest, you will be tasked with building a teleporter and entering the Institute. If you want to join the Institute, then it doesn’t matter what faction you work with to build the teleporter.
Once inside, you will walk out of the relay room to hear a voice on the intercom system. He will invite you to come and meet with him. You will see an elevator ahead of you which will take you to him. You will get your first glimpse of the Institute’s operations as you move down.
The elevator will stop, and you will step out to find a room with a small boy who turns out to be a synth version of Shaun. After some dialogue with him, the mysterious Father will come in to speak with you. You will learn that he is actually Shaun and that time has passed many years since you saw him taken. Be careful not to upset him during your conversation, as you can become hostile to the Institute through dialogue. He will offer you the chance to join the Institute although you can postpone the decision and join later
As the last part of the main story mission “Institutionalized”, you will have to go and meet with the four Institute department heads. You will be able to fast travel in and out of the Institute once you have completed this.
Your first mission with the Institute will involve tracking down an escaped synth. You will have to travel to Libertalia to meet a courser. Once you have rendezvoused with him, you will have to make your way across the hazardous pathways made from boats and scrap. There will be many raiders along the way hiding in nooks and crannies. The target will be in the main structure in the back. To get there, make your way to the lift that is attached to the structure by cables.
Be careful when approaching the lift and riding it. One of the raiders will be launching mininukes at you. After clearing the rest of the raiders, you can talk to the rogue synth. If you do not convince him to return to the Institute, you will have to kill him.
You can now return to Father and inform him of what happened. Afterwards, he will allow you to visit your new quarters. It will contain a bed and some storage space.
The Battle of Bunker Hill
There are some synths being held at the market at bunker hill. You will have options to tip off the Brotherhood of Steel or the Railroad if you want to help them. You will arrive and meet a courser. After speaking with him, a battle will ensue between The Brotherhood, the Railroad, Institute synths, and super mutants. You can kill anyone while the battle is raging without any of the factions turning hostile. This is a great opportunity to take loot from the dead soldiers.
You can complete the quest by either killing the courser or finding and resetting the synths. You can kill the courser at any point as long as the battle is ongoing. If you want to reset them, you will have to make your way into the monument from the back. There will be a hatch that will take you to the synths. Simply reset them and return to speak with Father.
He will be standing on top of the ruins of the CIT. If you killed the courser, you will have to be very careful with your dialogue. If you admit any guilt, Father will turn against you. After this conversation, the quest will be completed.
Father will request your presence at a meeting between the department heads. Father will break the information that he is dying. After the shock of those in the room, he will then announce the sole survivor, you, as his successor.
This quest will cause you to become enemies with the Brotherhood of Steel. You will have to speak to Dr. Filmore, and then head to the relay room. You will be teleported to the top of the mass fusion building. You will find a keycard in a room upstairs. Afterwards, you can use the elevator to descend into the mass fusion building.
As you descend, waves of Brotherhood soldiers will appear on the multiple levels of the building. The elevator will break down about halfway to the bottom. You can repair the elevator or make your way down on foot. Either way, you will have to fight a lot of soldiers. Once you make your way to the ground floor, there will be a door on the left side of the room that will lead to another elevator which will take you to the reactor chamber.
If you aren’t wearing power armor, you will want to pop some rad-x and have some radaway ready for this next bit. You will have to step into a room on the left of the control room. There will be a button for you to press which will close the doors and decontaminate you. When the other door opens, rush up the stairs and activate the Reactor. The rads will be pouring on. Once you take the beryllium agitator, a couple of turrets will begin firing on you. Quickly take them out and make your way back to the decontamination area.
The control room will be invaded by a small army of synths and robots, the toughest being a sentry bot. You will then have to fight your way back to the elevator. There are doors on the ground level that you can use to exit the Mass Fusion building.
You will be tasked with retrieving a scientist who has been living in Greygarden. You will arrive to find the Minutemen waiting outside to help him. You can talk to their leader and try to resolve the situation without violence if you want. Do not order the Minutemen to attack if you want to stay allied with the Institute.
Whether you kill the Minutemen or not, you will find some Institute members inside. Dr. Wallace will be holed up in a room with a locked door. You can try to convince him to give up and join the Institute or order him to be taken by force.
Father will ask you to make a speech to the people, not just of the Institute, but of the whole Commonwealth. You will first have to record your speech into a microphone Father has set up for you. You can stick with the prewritten “nice” sounding options or go off the rails a little. Its your speech, so do what you choose.
You will then have to broadcast this message to the Commonwealth. You need to travel to Diamond City and find the radio station. The operator won’t like what you’re doing, but he will not intervene. You will have to insert parts into the transmitter. You will find the parts in the station. There are three parts and three slots, but it does not tell you which goes where. You will notice a lighting system, however. Each correct part will light up one green light. Its merely trial and error using the green lights to determine the correct piece and switching out the others until they are all in the correct slots.
You will then return to the Institute to find Father in the reactor room. Now that the beryllium agitator is in place and the speech is being transmitted to the Commonwealth, its time to start the generator. Just open the door and activate it.
You will then have to go to the conference room and host a meeting. This is your first chance to show the Institute how you’re going to lead them. You will have a couple decisions to make and will be questioned by them, but you don’t need to worry about saying the perfect thing. Just address them as you wish.
End of the Line
Shaun will tell you that you need to end the Railroad. Not only are they opposed to the Institute, but you also need to prove that you are not loyal to the Railroad.
If you are still on the Railroad’s good side, you can teleport inside. If not, just enter through the Old North Church. You won’t face an army of Railroad agents. The main characters from the Railroad will be inside the HQ. P.A.M. will not attack you unless you attack her first.
The Brotherhood of Steel
is next on Father’s hitlist. If you have already taken them out, then this quest will not be necessary. The Brotherhood are going to put up much more of a fight than the Railroad. When you arrive, you are going to face heavy resistance at the airport. You will first need to destroy three generators which will be marked by waypoints. One of them will only be accessible by using an elevator.
You will then have to make your way to Liberty Prime. Climb the stairs to the back of his head. A synth will arrive and begin working on Prime, and you will have to defend him. Once he is done, Prime will begin going through some dialogue and will then shoot lasers at the Prydwen. You will be relayed to a safe distance, the Prydwen will fall, and the Brotherhood will be finished.
Father, your son, has run out of time. Its his time to pass, but your time to take over. After you speak with him, he will pass on and you will officially become the leader of the Institute.
You can continue completing minor quests for the Institute and exploring the world.
These quests are simpler than the main faction quests. Most of them are repeating quests from the various doctors. You will have to speak to them individually to receive their quests. Instead of drawn out guides, there are important tips for each.
- A House Divided: You do not need to kill the doctors. Killing the synths, turrets, and doctors will not affect how people view you. If you do not pass Doctor Higg’s first speech check, simply unlock the door with the holotape and speak to him again. Dr. Loken will open the door. You can also just let the synthetic gorillas kill all of them or kill Higgs and Loken yourself.
- Building a Better Crop: When you find Roger, make sure his family does not find out that he is a synth. When Bill and Roger are in their standoff, you can try to convince him to stand down, but killing him will work as well.
- Plugging a Leak: This quest is easy to miss. If you have completed “Tradecraft”, this will be unavailable. If you want to stick with the Railroad, then frame Dr. Ayo. Otherwise, just turn Binet in. You will receive a fairly hefty amount of caps.
- Political Leanings: This quest is as simple as it sounds. Just get the report from the mayor and return to Dr. Ayo.
- Appropriation: Dr. Watson will send you to various locations to take blueprints from Brotherhood members. These quests will not make the Brotherhood of Steel turn against you.
- Hypothesis: Dr. Holdren will send you to a super mutant infested area to kill one specific mutant and collect a tissue sample. The mutant will have an objective marker pointing you towards him.
- Pest Control: Dr. Binet needs you to simply kill ghouls at various locations.
- Reclamation: You only need to fight your way to a synth and attach the device for Dr. Secord.