This sidequest will trigger automatically after destroying the Prydwen in the quest With Our Powers Combined. You have to deal with waves of vertibird attacks. If your defenses are already heavy enough, you just need to sit back and relax as your turrets rip their vertibirds in the sky. Another option is to snipe the pilots with VATS to make the vertibirds crash. Having MacCready's headshot perk and the Penetrator perk Rank 2 is quite devastating against the helpless pilots.