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

The Institute

- Mission aside, you now get a chance to explore. You’ll hear a voice when you arrive that will give you the Institutionalized quest all proper like, and it will suggest getting on an elevator. Look around the immediate room for items, then head down the stairs nearby and hop on the elevator as suggested.

- Follow the path laid out for you by Father. Super spoilers ahead. At the end of the conversation Father will ask you to join the Institute; if you’re not sure of yourself you can waffle and have a chance to look around, though even if you say ‘Yes’ you can change your mind later. If you do say 'No' several times you'll be kicked out, though you still have until you return to the teleporter room to recant to Father. (There's honestly not much point in turning him down, unless you think it's 'in character'.)

- You’re now free to wander around the Institute and see all there is to see. Start by checking through the door behind Father. There’s a two-floor series of offices and labs beyond with plenty to nab, if you’re looking for raw materials. There’s a Novice terminal on the second floor; you can either hack it or check the desk beside it for Father’s Terminal Password. (Not quite the same name, but spoilers.) The terminal has lots of info of interest, but nothing of practical use.

The Institute of Fallout 4.
Behold its supreme cleanliness.
- The door across from Father leads deeper into the Institute. Head downstairs and you’ll find a central hub of sorts that leads to each of the Institute’s various sections. You’ll find the following in each area, working clockwise from the top:
  • In the north you’ll find the Commissary, a small eatery. You can purchase Institute Bottled Water and Institute Food Packets. Oh man, what selection. Head north through here and you’ll see a sliding door beside the stairs; this leads to a rear set of storage rooms containing all sorts of nifty junk you won’t find elsewhere in the game. (The Institute is packed with stuff to Scrap, frankly.)
  • Up the stairs to the northeast is Institute Bioscience. This is a laaaaarge area with lots to see and lots to grab, both in the main area and down the jumble of connecting hallways. In the main area you’ll meet the rude Isaac Karlin and the genial Clayton Holdren. Holdren will promise missions later, if you join up with the Institute. Check the side storage areas (first right when you enter Bioscience) and, along with a locked storage room, you can find a path into the FEV Lab. There’s another in the main area, but it’s behind a Master terminal, whereas this one’s just a Novice locked door. The FEV Lab contains the cure Virgil wanted you to grab, among other things.
  • In the east is a requisitions Synth who will sell you a variety of arms, armour, and other items. The selection is small, but there’s some really neat stuff you’ll only find in the Institute on this dude. Near him is a Master locked terminal and accompanying sliding door. (I don’t know where this goes, but given the geography, I suspect it leads to the FEV Lab.) You’ll usually find Allie Filmore, the head of Facilities, wandering around in this area, either on the ground floor or up the stairs to the apartments.
  • Institute Robotics is in the southeast. Here you can meet Max Loken and Alan Binet, two dudes obsessed with Synths. There’s not much to see here right now.
  • To the south, besides stairs up to the apartments looming over everything else, there’s a small storage room. In the rear of the room you can find an elevator; it leads to a small dig site. There’s not much to see up here besides the occasional tool and implications.
  • To the southwest is the Institute SRB, and you’ll probably find a dude named Newton Oberly arguing with a Courser. In here you can meet Justin Ayo and Alana Secord, and learn more about Coursers in general. This area has an appreciable amount of ammo laying around in the side rooms. The terminal on the lower floor has a mind-blowing revelation about an NPC that you should not miss.
  • In the west is Dean Volkert, the resident physician. He can patch you up. There’s a Novice locked terminal nearby; using it to lock the door next to the terminal will net you more stuff. As if the Institute wasn’t jammed with stuff already.
  • In the northwest is Institute Advanced Systems. In here you’ll find Rosalind Orman and Evan Watson. They’re both moderately weird. In a back room to the right is Madison Li; speak to her and she’ll install a Courser Chip in your Pip-Boy, allowing you to fast travel in and out of the institute without having to use the Signal Interceptor every time. Check her desk for the Advanced Systems Notes Holotape. There’s a laser-blocked doorway in the rear of Advanced Systems which may, some day, take you to the final battle of the game.
In addition to the stuff on the ground floor there are three upper rings of apartments, with one or two per floor. That makes a grand total of… well, a lot of rooms to check. Eesh. Most of them have the usual amenities and aren’t much use, but two have things of interest:
  • There’s a copy of Astoundingly Awesome Tales in the apartment on the top floor of the northern cluster. Look on the balcony to find the magazine.
  • There’s another Advanced Systems Notes Holotape in the apartment on the top floor of the western cluster.
In order to complete this quest you need to specifically speak to four people: Allie Filmore, Clayton Holdren, Justin Ayo, and Madison Li. Once that’s done you’ll gain a new quest, Synth Retention, and gain the ability to fast travel out of the Institute.

You now have a quest to complete for the faction with whom you sided in The Molecular Level. What you have to do for this small quest varies from faction to faction. It's worth noting that you can still complete these quests after choosing a side in The Molecular Level, though you'll have to complete Institutionalized and leave the Institute first. Speaking to the faction leader (Preston / Desdemona / Maxson) will let you access the quest in each case. If you decide to go with the Institute, of course, you can ignore these quests completely.

Inside Job (Minutemen) / Outside the Wire (Brotherhood of Steel)

Right outside the teleportation chamber is a computer8terminal. Load the Network Scanner Holotape Sturges / Proctor Ingram gave you before the jump into the computer, initiate a scan, and pull it out again. Give it to Sturges / Ingram once you leave. It’s… it’s that simple. Note that you cannot leave the Institute until you've done this.

Underground Undercover (Railroad)

The Railroad's task for you is more complex, as they have an 'inside man' at the Institute. It's a more complex quest as a result. (I'll fill this in when I get a chance to complete said quest.)

From Within (Brotherhood of Steel)

The Brotherhood of Steel has two quests for you to complete, and, like the task for the Railroad, it's not easy enough to just plunk down here. 

Decision Time

Institutionalized is the last neutral main quest you’ll undertake in Fallout 4. After this point all quests you encounter either won’t affect the storyline much at all, or they’ll completely affect the storyline - and begin the process of burning bridges between the factions. In essence what you’re going to do soon is choose one of the four factions - Minutemen, Brotherhood of Steel, Railroad, or Institute - and side with them in a war against the other three. The Minutemen always come out fairly unscathed on the other side, but the Brotherhood, Railroad, and Institute all face potential destruction, and once you complete certain quests for one faction you’ll lose the ability to interact with the other two factions in the post-game content. Usually because they're dead.

Just to be clear, you are not locked into a decision yet, nor will you be by undertaking Synth Retention for Father. Nevertheless, if you haven’t been eying one of the factions in particular yet, now’s the time to start thinking about which side you want to join.