THE INSTITUTE QUEST 04 - Mass Fusion
Triggered upon completion of The Institute Quest 03 - Mankind Redefined
Note: During this quest, if you side with The Institute you will be fighting large amounts of Brotherhood of Steel troops as well as multiple bot enemies. Equip yourself with gear accordingly (power armour and energy weapons).
Objective: Speak with Allie Filmore
After tracking Allie down (to her bedroom in my case), she'll tell you that the planned reactor needs a part. A beryllium agitator. She also plans to accompany you to the surface to oversee transport of the pre-war tech. You can convince her to stay behind or take her along for the ride (she acts as another gun during the mission, so there's no real downside to bringing her).
(Choice) Objective: Relay to Mass Fusion
Take the central elevator back up to the relay control room and here you'll be presented with your choice. You will be warned by the game as you enter the relay. If you use the relay to travel to the Mass Fusion facility, the Brotherhood of Steel will become hostile to you. You will align yourself with the Institute (although you can still side with The Railroad later if you are pursuing their questline). This also triggers the Steel Shutdown Brotherhood of Steel sidequest.
(Choice) Objective: Or inform the Brotherhood
The other option is to travel to the Prydwen/ Cambridge police station and tell the Brotherhood of Steel all about it. Doing this will begin the Brotherhood of Steel Quest - Spoils of War.
Objective: Locate the beryllium agitator
After the light vanishes and you rematerialize, you'll be on the rooftop of the Mass Fusion building. There are around five Brotherhood troops scattered around the roof, including a couple in power armour. So use the few seconds you have to take cover. If you manage to avoid being detected, try to take out one of the patrolling power armour enemies with a stealth attack to make things easier. The Brotherhood troops are heavy on grenades which can be a real problem on higher difficulties, so make sure to use med-x or power armour if you are having trouble.
Advance into the building to finish off the scribes inside and you'll find a cylindrical elevator in the middle of the room with a key card reader inside. Take the stairs to the second level and enter the workshop on the other side of the room. In the corner is a terminal you can interact with to gain access to some internal messages that point out the location of the agitator (the lowest level of the complex obviously). You'll also pick up the location of the key card used in the elevator. If you can't access the terminal, you can find the password in a desk just outside the door of this workshop, along with the keycard.
Objective: Retrieve the executive keycard
Note: When you descend in the elevator, you will want good energy resistant armour on or power armour as you are about to be ambushed and there is no cover.
Grab the keycard from the wooden desk on the upper floor and then return to the elevator below to run it through the reader.
Objective: Proceed to the reactor level
As the elevator slowly descends down the structure, Brotherhood knights and scribes will run out of doors on most floors and fire at you. On higher difficulties, you'll need to be quick on the trigger or use some stimpaks to keep healthy or else the chip damage can be dangerous. The slow ride will continue for a good minute or so until you finally come to a halt.
Depending on your HP situation, as soon as the elevator stops you may want to sprint for the doorway to the right to get into cover. This is because a power armour knight and several other enemies will be firing at you when you step out of the elevator. Once you are in cover, you can sort out your health and start fighting back properly. Work your way through the rooms, cleaning them out one by one
(Optional) Restore power to the elevator
To restore power, you'll need to find a ramp leading up to the level above and then cross to the other side of this upper floor to find the marked circuit breaker. There's also an expert lock safe in the same room you can plunder for items as well. Reactivating the power allows you to take the elevator down to the lobby below. There's an expert difficulty locked door on the lower level as well that allows you to simply fall down holes in the floor instead, working your way down floor by floor.
You can find a key for this on a desk beside the development manager's terminal in a side room of the lower level if you can't lockpick the door. This slow descent is a safer approach on higher difficulties as you have control over cover and dealing with enemies but the choice is yours. Either way, descend all the way down and deal with any enemies you encounter.
Note: The slow descent method will also allow you to find the strength bobblehead on level 5 by looking down onto a railing that overlooks the lobby below.
When you finally get to the lowest level, use the marker to find a nearby elevator that will take you further down into the depths of the building to the reactor level.
Objective: Retrieve the beryllium agitator
Work your way down until you can see into the reactor chamber through the large windows. On the upper ledge to the left when you are looking towards the reactor through the window is a red loot chest for you to empty. Make sure you check the side room here for a hazmat suit, as the reactor has extremely high levels of radiation (you'll take about 90+ radiation damage a second without power armour or a hazmat suit) so make sure you are prepared. You can also loot the master lock safe the suit is sitting on if you have the required skill.
Entering the side passage to the left will place you in a decontamination chamber. Activate it by pressing the button and wait for all your rads to vanish (this is handy if you have taken a bit of radiation damage). When the reactor doors open, you'll enter a large chamber with the reactor in the center. Use V.A.T.S to locate a pair of laser turrets on the ceiling behind the reactor. When you take the agitator, these will trigger and fire on you. You can't damage them yet, but be ready to deal with them immediately when you get the item.
Objective: Take the beryllium agitator
Wind your way up the catwalks and interact with the reactor to retrieve the agitator from the reactor.
Objective: Eliminate reactor level security
As soon as you take the agitator, start firing on the laser turrets above. If you're wearing power armour they should pose little threat but the hazmat suit provides little protection against energy weapons. When they are scrap, backtrack down the catwalks and enter the decontamination chamber once again. Make sure to re-equip your best armour here as several security robots will assault you as you leave the decontamination chamber.
A laser turret will start firing down from the ceiling, then a sentry bot and protectron will arrive from the side rooms making life extremely difficult for you. Remember that you can retreat into the decontamination chamber if you need to and seal the door to gain time to recover. After the initial bots fall, a pair of assaultrons will run in from the far end of the room. These move extremely quickly and deal large amounts of damage on higher difficulties making them very deadly. Use your best weapons to bring them down fast before they can do the same to you. A final laser turret and protectron will be waiting to attack you as you work your way back up out of the reactor level.
Objective: Exit Mass Fusion
(Optional) Objective: Assist Institute forces in the lobby
Ride the elevator back up to the lobby level and enter the door to your left to find Institute forces duking it out with the final push from the Brotherhood. You can sit in the doorway if you wish, taking potshots or join in the fun in earnest. Or you can simply sprint past the combatants and through the marked doorway on the right to exit the building. Your call. Fast travel back to The Institute when you are outside.
Objective: Talk to Allie Filmore
Track down Allie and hand over the beryllium agitator to wrap things up and finish off this quest. Whew, that was 'interesting' on survival difficulty. This will also start you off on The Institute Quest 05 - Pinned as well.