Story Related, Unmissable
Once you've left Smith Casey’s Garage, either Fast Travel back to Rivet City or walk back and escort your Father. Personally I prefer to Fast Travel back and waiting in game time for your Father to appear in the lab as he's invincible and cannot be killed (just knocked out), it's also a lot faster than walking.
Once your Father appears, return to Dr. Li in the Science Labs and wait for him to persuade her to re-activate Project Purity. Once everything is agreed you'll be asked to meet everyone outside the Gift Shop entrance at the Jefferson Memorial.
Before the team can enter, you have to kill all the remaining Super Mutants. If you eradicated the Super Mutants on your previous visit then everyone will have already setup and be preparing to re-activate Project Purity. Your Father will ask you to do 4 things before they can begin, once you've accomplished everything he has asked you to do you'll see a load of Enclave Soldiers arrive in a Vertibird.
The Enclave now stand between you and your Father so make your way quickly to the Rotunda, killing everything that gets in your way. After you’ve returned to the Rotunda and seen and done everything there, you'll be asked to Escort Dr. Li and a few others out of the Memorial, through the Sewers and out to the Citadel. Once you get to the Citadel, Dr. Li will argue with Paladin Bael over the intercom, then you’ll be let in. The trophy will pop once Elder Owyn Lyons has finished talking.
Once you leave here, you will be unable to return until the quest "Take it Back!", The Jefferson Memorial will also disappear from the world map and become inaccessible due to the Force Fields that the Enclave will put up.