Tell Preston you’re “Ready to attack” and you two will split duties. Fast-travel back to Sanctuary to talk to Sturges and you’ll learn that The Institute bring in water from the old sewer systems under C.I.T for their reactor, and that is your way inside. Sturges will also give you the key item “Institute Relay Targeting Sequence” which you will need to use once you are inside The Institute in order for you to warp-in allies.

Now there are two ways to get to your destination in The Commonwealth. The game wants you to travel to the C.I.T. Ruins, but if you do that you will have to travel quite a ways east, fighting through a couple of Raider camps along the way. Easy enough to do, but your target is just south of Ticonderoga so you can alternately just fast-travel there. Either way, once you get to the top of the north-west bridge, you will see the objective marker is down in the river. Heh, yes you are going for a swim. Pop a Rad-X and leap in, heading for the marker to see a pipe leading from the river onto land. Follow it to enter the “Public Works Maintenance Area”.

Public Works Maintenance Area¶

Sneak into the Institute via the Maintenance Area. Emerge into this first room as both of the pipes here have grates over them. Use the keypad on the wall and the left pipe’s grate will open up. There is also a locked terminal [Advanced] here you can hack to open up and claim a Steamer Trunk (quite nice!). Continue down the pipe you opened up and you will soon be dumped down into the sewers.

Well, so much for an exit strategy. Get out of the cesspool and take out the two Laser Turrets up ahead to the south. Keep following the path through the pipe you find. At the end it may look like a dead-end, but open the hatch you find on the left and you can get out easily (you’ll have to deal with more of these hatches, by the way). Head upstairs here and look for a First-aid Kit with a lock [Novice] on it. There’s plenty of junk up here too. Continue on to another sewer section and you’ll have to travel through some sewer tunnels. You will very likely find a Mole Rat or two at the start of this area but continue on and that will turn into Feral Ghouls. Fight your way forward to a four-way split where you will fight a number of ghouls. The only way forward is to go left (the other paths are dead ends), but there is also a Glowing One down there. Once you see him, hit him with everything you have. The LAST thing you want is to have the Glowing One charge into the middle of Ghoul Corpses and use his ability to resurrect them all, so take him out fast.

Continue on down the left path to another split. To the upper right is a Laser Turret you should take out. The left path is a dead end but you can find a suitcase and a First-aid Kit down here. Grab it all and head down the right path, but once you get to the walkway/stairs go into sneak mode. Up ahead in the room past the hole you will see two Synths working on repairs. Go ahead and kill them both with a silenced weapon to take care of two upcoming threats.

Now here there are two ways to continue. You can hack the Terminal [Expert] here for a shortcut, but hack it for the XP if you can and then continue southeast up the tunnel (you are going to go gather a few items). You will find a hole in the wall up here that gets you into the maintenance rooms just as well. Enter the room and to the left you can find a Fusion Core and a locked security door [Expert]. Once again, pick it for the XP if you wish, but head back and go north-east through a door and up the stairs. Kill the Synth up here and then check out the computer terminal (the Robotics Terminal). You can read the logs here which talk about kids using computers with fake names and then you can read “4n1m4l’s test logs” to see that he basically destroyed a robot on a treadmill. Ha. Eject the tape to receive “4n1m4l’s test logs”. You can see the robot destroyed down below, but to the left is another terminal [Expert] you can hack for some goodies and a small room to the right of that with an ammo box. The robot that was destroyed down below is an Assaultron and you can loot it for some more goodies.

Head back up the stairs to the Robot Terminal and go north-east to a hallway. Just to the right is an elevator (broken down) with an ammo box. Head onward and in the room up ahead on the right there are… just a ton of monkeys.

Why are there so many monkeys? The developers are really having fun here! The desk in here has a First-aid Kit and an Overdue Book you can pick up for the Boston Library book return. There is also a locked safe [Novice] on the wall behind the desk. Exit and continue down the hallway. The left door is the only way forwards thanks to the rubble, but there is likely a Synth waiting for you. Kill it off and note the hole in the wall to the left that connects to the robot testing area. Head past it and further down is a machinery area. To the left here is the expert security door that you may or may not have picked from earlier. Go right now and loot the room you find (there’s lots of junk) and then continue past the “Restricted Area” door.

In here the left path leads down to where the expert terminal was from before. You can find some laser pistols on the desk down there, but continue north to a walkway with plenty of junk and a locked toolbox [Novice] on one of the shelves. Head down to where you killed the Synths from earlier and you’ll have no choice but to head back into the pipes. Thankfully your pipe-time is drawing to a close. Jump in and follow this pipe and it will lead you directly into The Institute.

The Institute¶

Jump out of the pipe and you will find yourself in the Relay Room, down in the small maintenance area. You have access to the Relay Terminal easily from here and for some reason the room is completely empty. Go to the terminal and use the “Institute Relay Targeting Sequence” to call in the rest of the Minutemen (or at least Preston, Sturges and some back-up). Talk to Preston here and he will give you a “Fusion Pulse Charge” to attach to the reactor and will then tell Sturges to get used to the warp drive controls so he can warp us out of this place once you are done. He also gives you an optional objective to issue an evacuation order to try and save as many lives as you can. Now that you have your backup, follow the objective marker and enter Old Robotics to continue.

Old Robotics¶

Use the Terminal [Advanced] you find here to turn off the turrets and continue. You are going to run into pickets of Synth Resistance along the way, but you’ll be overpowering them fairly easily (A quick tip: shoot off the Robot’s Right Arms - they will drop their guns and be much less effective as they try to melee). As you go down the stairs here you can target a turret in the far distance (you can snipe it; apparently the terminal doesn’t shut them all down), but follow the linear path downstairs. Synth Striders may be down here, so chuck a grenade downstairs to help blow them apart. There is a room on the left down here where you can hack another Terminal [Advanced] and turn off the turrets (there is a First Aid Box nearby as well). The room across the way has an Explosives Box you can loot. Keep heading down though and you’ll see another terminal and a door on the right leading into a bathroom (go there first for the First Aid Box).

This terminal is the “Prototype Sequence” terminal. Turning it on will unleash a (hostile) Sentry Bot that will attack the two Synths here. Let them fight it out, but sneak up into the room on the right. As you advance into the room, two more Synths from the right will show up, giving the Sentry Bot new cannon fodder, but by now your allies are likely fighting as well. Focus on the Sentry Bot and take it down, then wipe up whatever it didn’t kill. Follow the path on the right to a hatch. Open it and drop down. This leads to a lower room where you can pull a Fusion Core from the machine. Continue to follow the path (note the Explosives Box on the left) and you will soon come to the “Institute Bioscience” room.

Institute Bioscience¶

Now this room is going to be chaos. Head out into the main room and kill any scientists you see (they are level 1). Out in the main room though, you will face a wide variety of enemies, including turrets on the ceiling, various Synth enemies, scientists running around, and GORILLAS! Yes, the caged Gorillas they keep here will be let loose, attacking only you. The first things you should take out are the annoying turrets. There are two on each side of the room, but they have a large radius of fire, so shoot them down while circling the room. Wipe out all the threats here and continue on to “The Institute” proper.

The Institute, Continued¶

Bioscience may have been chaos, but this area is utter madness. There are quite a few enemies blocking your path here, but you will at least have your Minutemen allies. You will need to fight your way to the elevator. The majority of the areas around you are blocked off, so this is a fairly restricted area, but you will likely fight some Coursers and other levelled Synth enemies. Of special note is “XPN-20A”, a legendary enemy that will appear here. Again, try to take out his weapon and if you are looking for respite try jumping down into the water areas (he doesn’t like to follow). With all the help you have you will take him out fairly easily.

Fight your way forward and wipe out all resistance and once you’ve cleared the area Sturges will announce on the speaker that you need to head to Advanced Systems, but to do that you need to use the Director’s Terminal to undo the lockdown. Head to the elevator now and you’ll be on your way to Father’s Room. Head inside and go up the stairs. Now, here you should quicksave and put on your CHR gear. Go talk to Father now and he will be very saddened (as you can imagine). After a bit of dialogue, you have the option to tell him to help you, a moderate speech check. Pick it and he will ask why. This is another moderate speech check, with various choices though. Pick whichever one you want and if you pass it he will give you the Synth turn-down code, 9003. Use the terminal here now and pick every option which turns on the evacuation notice, turns off the lockdown, and finally shuts down some Synths with the code you just got.

Head out the door nearby and go down the stairs now. Make your way to the large room (where more fighting has broken out) and head for the Advanced Systems.

Advanced Systems/The Reactor¶

This initial area has a few scientists still hostile, namely T.S. Wallace. Take down any threat and fight your way forward to the reactor. Once you load in, hang a right and head up the hallway, taking out the three laser turrets they have put in place. Continue down to the bottom and the reactor room, which is filled with scientists and enemies. There are TWO named Legendary Enemies here: Z4K-97B and A-2018. Z4K is on the bottom and should be dealt with first. Fire on him from outside the room and if he comes inside let your allies trip him up as you hurt him.

Once he is gone, clear out the bottom and pick off any low-level enemies down below. Now, to easily handle A-2018 you can actually sneak up the right side stairs and sneak attack him from there (or at least hurt him without him knowing what is going on). It is a bit sad but you can take him out easily. Be sure to loot either Z4K-97B and A-2018 for their legendary gear AND to find one (of the two) “Reactor Terminal Password” items.

Now all that is left to do is to use the terminal and shut down the reactor. After that, go interact with it and place the Fusion Core. Talk to Preston afterwards and you will be warped back to the relay. Here you will have a choice to make: the young synth Shaun has shown up, asking to go with you and recognizing you as a parent (unlike before). You can choose to take him with you or leave him behind (which is basically getting rid of him). The choice is obviously yours, but you get more utility out of taking him with you.

Make your choice and talk to Sturges and soon you will be warped to the Mass Relay building, by a pre-rigged detonator (which the Minutemen say is the best place to trigger the explosion from). You know what has to be done here, so go ahead and do it. Watch the fireworks as the Institute (and CIT Ruins and some of the surrounding area) are wiped off the map). For the good of the Commonwealth! Talk to Preston now and your quest will soon end, finishing the main storyline of the game. Congratulations, General! You can, of course, continue to journey the Commonwealth and complete anything you have left unfinished.