Archer and the crew are on Earth for a historic conference at Starfleet Headquarters to establish an interplanetary coalition. But the plans are menaced by a fanatical xenophobe, John Frederick Paxton. He leads Terra Prime, an underground Human isolationist movement plotting against the government and threatening to undermine the talks. This radical faction opposes the increasing number and influence of aliens on Earth and advocates expelling all non-Humans from Earth and the rest of the Sol system.

Commander Riker interacts with Archer's crew in a hologram of their final mission as he deals with a dark secret from his past. Six years after the Terra Prime incident, an emotional Captain Archer and the crew return to Earth to decommission Enterprise and sign the charter for the Federation, the new alliance of planets they helped forge. Enroute, Archer agrees to help his old ally Shran retrieve his daughter as the captain prepares a speech to celebrate the Federation's establishment.