With Liberty Prime nearly ready to help assault the Institute forces, a final component is needed, in the form of a Beryllium agitator. Now it is a race against time, as the Institute are also actively searching for the agitator, and have already infiltrated Mass Fusion before the BoS can arrive.
Speaking with Proctor Ingram will reveal that Liberty Prime needs a final component in order to reach fully functioning capacities, with the component needed, being in a hidden area within Mass Fusion. However, the Institute have already reached Mass Fusion, and so the BoS are sending in the Sole Survivor in order to take down their forces and retrieve the Beryllium agitator first.
At this point, the Sole Survivor has one final chance to ally themselves with the Institute over the BoS. Warning Father of the Brotherhood's plans, will permanent make the BoS hostile, and will begin the quest: Mass Fusion.
Allying with the BoS, the Sole Survivor will arrive at Mass Fusion via Vertibird, and will gain access to the building through the roof. As the Sole Survivor travels down into the building's depths, they will be forced to deal with a large synth presence, in order to reach the executive research lab terminal, where they can obtain the necessary Mass Fusion executive lab password and Mass Fusion executive ID.
Afterwards, restore power to the nearby elevator, by either hacking the respective terminal, or by heading back up to flip the circuit breaker.
Once the elevator has been powered up, the executive ID card can be used to access the basement level, where the Beryllium agitator is being held.
After going through the decontamination chamber, grab the agitator, in which the building's automated security will activate, forcing the Sole Survivor to deal with their presence in order to take the elevator back up to the lobby.
Upon reaching the lobby, a fight between Brotherhood soldiers and the surviving synth forces will be encountered, in which an optional objective will appear, in which the Sole Survivor can help the BoS take down their opposition.
After Mass Fusion has been cleared, return to Proctor Ingram at the Boston Airport.
Speak to Proctor Ingram
I've been informed that Proctor Ingram once again has requested my assistance at the airport.
Fly to Mass Fusion
In order to restart Liberty Prime's reactor core, I need to recover the "Beryllium Agitator" from the ruins of Mass Fusion. I should board a vertibird and head over there as soon as possible.
Jump to Mass Fusion's Roof
Locate the Beryllium Agitator
Proceed to the Reactor Level
One of the terminals at Mass Fusion has indicated that the Beryllium Agitator is located in the building's basement reactor. I'll need to find a keycard to access the facility's executive elevator.
(Optional) Restore Power to the Elevator
Enter the Reactor Chamber
After fighting my way through Mass Fusion, I've arrived at the Reactor Level. I now need to find a way to remove the Beryllium Agitator from the reactor.
Unlock the Reactor
Take the Beryllium Agitator
Mass Fusion's reactor is now unlocked, and should allow me access to the Beryllium Agitator.
Eliminate Reactor Level Security
Exit Mass Fusion
With the Beryllium Agitator in hand, I should head back up to Mass Fusion's lobby and exit the building.
(Optional) Assist Brotherhood Forces in the Lobby
Institute Synths are trying to prevent me from leaving with the Beryllium Agitator. I could help my fellow Brotherhood soldiers fight them off, or I could leave the building as fast as possible.
Return to Boston Airport
I've successfully helped the Brotherhood fend off the Institute Synth's attack on Mass Fusion. I should now bring the Beryllium Agitator to Proctor Ingram at the airport.
Speak to Proctor Ingram
Now that the Beryllium Agitator is safely in the Brotherhood's hands, it can be used to restart Liberty Prime's reactor core.
At this point in the game, both The Railroad and the Institute will be considered sworn enemies, and all future encounters with remnants of these factions will be seen as permanently hostile.