Ho sempre pensato che Phantom Liberty fosse un contenuto endgame, invece è roba integrata alla quest principale che ne modifica il corso e aggiunge pure un finale nuovo.
Mi ha già chiamato il numero sconosciuto che attiva la missione, ma leggendo in giro consigliano di aspettare e seguire questa scaletta:

That means you’ll need to complete Act 1, and the following Act 2 missions:

Playing for Time
Automatic Love
Ghost Town
Down on the Street
Play It Safe
Gimme Danger
Search and Destroy
Tapeworm

By jumping into Phantom Liberty at this time, you’ll be far enough in the main game that the new ending, which you can only unlock by beating Phantom Liberty, will actually make sense. That’s because depending on which endings you unlock in Phantom Liberty, there’s a chance the game will end right then and there for you. But by reaching Act 3, you’ll essentially replace the Act 3 missions and endings with Phantom Liberty’s creating a much more satisfying, and complete, story arc for V.