Enterprise visits an ancient Vulcan spiritual sanctuary, despite T'Pol's concerns that her human colleagues will be an awkward and disruptive presence there. Upon landing, they discover that the monastery has been forcibly taken over by the Andorians, a paranoid and highly excitable race of aliens with a long history of conflict with the Vulcans.

Archer and the crew are disappointed to discover that T'Pol has been ordered by the Vulcan High Command to leave Enterprise--and equally frustrated at her seeming indifference to leaving their ranks. T'Pol's last mission as a Starfleet officer, however, proves eventful when she and Archer are kidnapped by a militant faction on an alien planet.

Both the Vulcans and the Andorians make a claim to a small planet and military conflict soon erupts. As the fighting goes on, the Vulcans announce they are willing to discuss cease fire terms. However, Imperial Guard officer Shran believes only Captain Archer can be trusted to mediate the situation, which drags the Enterprise crew into the tense situation.

An Andorian ship led by Commander Shran arrives in the Delphic Expanse to help Enterprise hone in on the Xindi super-weapon.

Archer puts his life on the line in a risky gambit to intercept the Xindi superweapon and disarm it from within.

Archer, T'Pol and T'Pau attempt to bring the Kir'Shara — an artifact believed to contain Surak's original writings — to the Vulcan capital, as the NX-01 gets involved in a Vulcan-Andorian military clash.

Enterprise journeys to Babel with a Tellarite ambassador on board for peace talks with the Andorians, when a distress call from Shran is received.

Archer tries to unify the Andorians, Tellarites and Vulcans in a plan to capture a marauder ship threatening to destabilize the region.

Archer visits Shran's icy homeworld to find an Andorian subspecies called the Aenar, to determine their connection to the marauder destroying ships in the region.

Six years in the future, an emotional Captain Archer and the crew return to Earth to face the decommission of Enterprise and signing of the Federation charter.