Ride the vertibird and wait until Tom successfully docks to the Prydwen. Head inside and start killing everyone. Once done, head to the uppermost walkway where you can find the gas valves. Place the explosives there then leave the main deck.
Maxson and the last personnel on the ship will attack you. Destroy them and don't forget to loot Maxson's unique apparel, the battlecoat. Return to the vertibird and watch the Prydwen turn into a massive fiery wreck once you get into safe distance. Return to the HQ and talk to Desdemona to complete the quest.