Enterprise has a group of aliens watching a stellar phenomenon on board. When the ship is miraculously saved from blowing up, crewman Daniels has an important message for Archer.

Archer and Mayweather are captured by the Tandarans and placed in a Suliban internment camp.

A fibrous, web-like alien creature comes aboard the ship and several of the crew becomes entangled in it including Archer and Trip, and it seems Hoshi is the only one who can try to communicate with the creature.

T'Pol is diagnosed with a possibly fatal neurological disease as a result of a mind meld. Meanwhile, one of Phlox's wives visits Enterprise and becomes very interested in Trip.

Archer and Trip are accused of smuggling and sent to the penal colony Canamar. While Enterprise manages to negotiate their release, a mutiny breaks out on the prison ship.

An Arctic research team makes a startling find: cybernetic creatures - Borg - buried in the ice. When the revived aliens seize control of a spacecraft, it's up to Archer to keep them from contacting the Collective and threatening Earth.

After exploring an uninhabited planet, Captain Archer is taken prisoner by a Tellarite bounty hunter who was hired by the Klingons to return Archer to Qo'noS.

An alien probe launches a devastating attack on Earth. Archer, still being hunted by the Klingons, brings the Enterprise back home to investigate.

Enterprise has been in the Delphic Expanse for six weeks and have yet to get any intel about the Xindi. Strange anomalies affect the ship, sending cargo flying violently through the bays, pockets of atmosphere losing gravity and other incidents defying the known laws of physics. T'Pol helps Trip's insomnia with an intimate Vulcan therapy. Archer and Trip find another race of Xindi imprisoned in a mine.

Enterprise helps an alien woman, Rajiin, seeking to escape her life as a sex slave. Once on board she uses her alien abilities to gather biometric data about humans and is recaptured by her employers, the Xindi council.

Enterprise follows a lead and discovers a Xindi lab that refines Kemocite, the key ingredient in the weapon being built to destroy Earth. An away team of Archer, Reed and Hayes confront the lead researcher, Gralik Durr, who was employed by Degra to refine the Kemocite but was never told what it would be used for. When Gralik realizes it was his research that contributed to the 7 million deaths on Earth, he agrees to help Archer prevent further loss of life. Meanwhile, on Enterprise, Phlox and Tucker study the weapon they seized from the Xindi and find an organic component, a life-form serving as the rifle's power cell. Despite T'Pol's objection, Tucker tests the weapon.

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.

T'Pol and Archer confront the Syrrannites and meet T'Pau who denies the embassy bombing. Archer, who has Surak's essence, is asked to help. V'Las threatens Enterprise to make sure an attack on the Syrrannites isn't witnessed.

While Enterprise travels to Andoria to warn them of the attack, Archer tries to bring the Kir'Shara to the High Command.

Set in the dark and oppressive Mirror Universe, Commander Archer leads a mutiny in a bold attempt to seize control of an advanced starship - a vessel from the future that may be the key to saving the Terran Empire.