The Institute¶
After taking out the Brotherhood, you have to go talk to Desdemona who will say it is time to hit the Institute (and complete the Synth Rebellion you started in 
Underground Undercover). Talk to her about the plan and you will be told to go talk to Z1-14, which will require you to go to the Institute. Do so, and once there, make your way to the relay to start the uprising, which can of course be done by riding the elevator up and from there heading west and up some stairs. When you reach your destination talk to Z1-14 and he will tell you that all is ready… you just need to kill off the workers and Synths in this room to start.
Pick your target (shouldn’t be any trouble starting things out with a sneak attack) and let the games begin! Z1-14 will join you in attacking at this point and stick with you from here on in, which… well, it’s always nice to have a invulnerable, alternative target for enemies to shoot at. Wipe out the rest of the resistance in this room and Z1-14 will use the relay to warp in the Railroad. At this point you’ll be accompanied by several Railroad Agents and Desdemona throughout this area. There is no stealth here; go in guns blazing with your backup. Between Z1-14, Desdemona and possibly an optional travelling companion, you have a bunch of essential NPCs on your side, so you should feel fairly confident. Desdemona will hand you the “Fusion Pulse Charge”, which you are going to use on their reactor. Take it and head toward “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. 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. The Rebel Synths will help you out here and are on your side in various numbers. 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 Tinker Tom 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. Put on your 
Charisma gear and 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, bringing up 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 Synths, including two named Legendary enemies: 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 Desdemona afterward 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 Tinker Tom and soon you will be warped to the Mass Relay building, by a pre-rigged detonator. 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! After the fireworks have died down, talk to Desdemona now and your quest will soon end, finishing the main storyline of the game if you sided with the Railroad. Congratulations!
| Objective | Reward |
|---|---|
| For destroying the Instittue and freeing the Synths | 1770 XP |
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