After Silik attacked Trip, Vosk wants to make a deal with Archer: supplies of the ship for the completion of his time machine in return for a trip to the 22nd century.
The crew take some time off. Archer meets an old friend, captain Erika Hernandez. T'Pol takes Trip to Vulcan, with a surprise waiting. Phlox finds out Earth has become xenophobic.
After a Klingon ship is attacked, it's discovered the imprisoned Dr. Soongs genetically enhanced humans are responsible. Archer takes him to prevent a war.
After a bombing destroyed the Earth embassy on Vulcan, Syrrannites are suspected. T'Pol receives a map from her Syrrannite mother, leading into a dangerous desert, The Forge.
After crossing the desert and surviving the sand storms, T'Pol and Archer confront the Syrranites in the Forge. The pair meet T'Pau, who denies any connection with the embassy bombing and Admiral Forrest's death. Archer, now possessing the mental essence of Surak known as the 'katra', agrees to let T'Pau extract it, even after T'Pol's mother T'Les warns the ritual may kill him. Meanwhile Vulcan administrator V'Las is willing to destroy Enterprise to make sure an attack on the Syrrannites isn't witnessed. Former Ambassador Soval allies with Commander Tucker to try to ...
Noncorporeal aliens inhabit the bodies of Enterprise crew members to study how the crew reacts to a lethal virus infection that has afflicted Trip and Hoshi.
Enterprise agrees to escort Tellarite delegates to peace talks with Andorians. En route they rescue several Andorians who abandoned the ship Kumarr, who insist it was Tellarites who attacked them. When Enterprise is soon attacked by the same ship which now appears to be a Andorian ship, Archer must prove to the warring races that a third party must be setting them up to fail at their attempt at peace.
While Enterprise is at Earth, Phlox is abducted by the Klingons and forced to research a cure for a virus destined to wipe out the race. Reed is tapped by a secret agency and ordered to betray Archer. Trip transfers to the Columbia.
While Enterprise tries to bring Trip on board to reverse the malicious Klingon modifications, Phlox and Antaak find a cure for the virus that will not please general K'Vagh.
While attending conference on an alliance, Trip and T'Pol find out from a dying woman they have a baby. Investigation shows the woman was a member of the xenophobic organization Terra Prime.