After retrieving your father from Vault 112, you need to return to Rivet City to restart Project Purity. He now believes this is possible through what is known as a GECK, a Garden of Eden Creation Kit, which was supposed to have been deployed by the vaults after the nuclear outbreak.
James has a discussion with Dr. Li, and convinces her to assemble a team to enter the control room. However, if you haven't done so already, you will have to clear the building of super mutants. These super mutants are on the lower floor, located in the back of the gift shop.
You'll need to go back and forth between the lower floor and the control room - first you need to power the flood control system, replace the shorted fuses in the power room, and access the project purity mainframe to turn it on.
However, there is a blockage within one of the pumps. You need to enter the grate in the north-east corner of the first floor to reach the manual pipe control. Once you turn it, you see a helicopter land; when you make your way back to the control room, you will find that the enclave taken control of the building.
You now need to escort Dr. Li and the other scientists to the Brotherhood of Steel citadel through an escape tunnel. In the first tunnel segment, you will find a room filled with enclave solders trying to shoot you through a doorway.
In the second part of the tunnel, Doctor Li will stop you and inform you of Garza's heart condition. You need five stimpacks in order to keep him moving, but a speech check may allow you to substitute Buffout or leave him behind.
Some scientists may get killed when going up flights of stairs, as two enclave soldiers will attack from behind, with clear shots to your party.
After reaching the surface, Dr. Li will inform Elder Lions that she has arrived and to open the gate.