With the conclusion of Spoils of War, you now have a suitable power source for Liberty Prime. Speak to Proctor Ingram to trigger this quest. Go up the scaffold surrounding Prime and insert the beryllium agitator in its reactor port on the back of its neck. Return to the platform where Proctor Ingram is located and power on the war machine.
Now it's The Brotherhood's turn to take the fight directly to The Institute. Escort Liberty Prime on a 15-minute stroll through the streets of Boston, making your way to the ruins of CIT. You're welcome to help take out any Synths along the way, but Prime will eliminate most threats for you.
The Brotherhood knows that its arch enemy is under the ruins of CIT. Once there, protect Prime as it tries to create a hole leading to The Institute. Once that's done, jump into the hole to complete the quest.