You'll approach the Mass Fusion building from the air, which gives you the chance to let rip on some of the defending synths from the vertibird minigun. This will be the moment of no return for your friendship with the Institute. This quest will have now launched, and we want to follow Proctor Ingram up to the Prydwen, so we can get on a vertibird. She'll offer to come with you and grab the agitator for the Brotherhood. Find Proctor Ingram, and bring her up to speed on what's going on.
Rather than heading to the relay, we're going to fast travel straight over to Boston Airport.
Refuse her company, because we're not going to be completing this quest with her.
She wants you to head to Mass Fusion to retrieve a Beryllium Agitator, and she plans to join you for this. Head to the Institute first, to get this quest going, and speak to Allie Filmore. If you are returning to this point having already completed the Institute ending, then make sure to reload the save you made when you first started the Mass Fusion quest.