This Railroad all-hands-on-deck quest involves surviving a Brotherhood attack. Speak to Desdemona to start the quest. After repelling the initial wave in the headquarters, speak to Desdemona again. Then clean out the catacombs and the church. Talk to Desdemona one more time.
Now it's time to take the fight to the Brotherhood, all the way up to their airship, The Prydwen. The only viable transport is a Vertibird at the Brotherhood-occupied Cambridge Police Station. Meet up with Tinker Tom outside the station. You can clean out the base of Brotherhood troops before or after meeting with Tom.
Make you way up through the police station until you've reached the roof. Talk to Tinker Tom, then defend the Vertibird while Tom tries to fire up the transport. The minigun is especially effective in taking out the incoming ships. Then talk to Deacon to complete the quest.