Enterprise encounters a group of Vulcan civilians who have split off from the normal way of Vulcan life in an effort to explore their emotions. T'Pol is disturbed by the new visitors and warns the Captain that all attempts in the past to integrate Vulcan emotions into their lives has proven disastrous. Meanwhile, a message from Admiral Forrest leaves the Captain with the difficult task of trying to convince one of the visiting Vulcans to call home to speak with his dying father.

Tucker and Reed set out on a mission in a shuttlepod, as Enterprise is busy investigating an asteroid field. Disaster strikes while the pair are away, leaving the shuttlepod damaged and the warp drive inoperable. They manage to make it back to the rendezvous coordinates only to discover Enterprise was apparently destroyed when it crashed into an asteroid. With the ship seemingly no more, the pair are left abandoned in the middle of nowhere with only a few days of air remaining.

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.

While investigating a gas giant, Enterprise comes across a damaged vessel hovering in the atmosphere, and T'Pol, Hoshi and Malcolm board the vessel to investigate. However, once aboard, they are ambushed by a hostile female Klingon who hijacks their shuttlepod and strands them on the Klingon ship, which threatens to implode under the pressure of the planet's atmosphere.

The crew discovers a new planet with two races, one in desperate need of medical and scientific assistance. In the course of trying to help, Dr. Phlox recalls his own Denobulan past to address the ethical dilemmas that arise in the present.

When Enterprise is attacked by an unidentified enemy ship, the crew must work frantically to get their new phase canons to operate. Meanwhile, the captain charges Hoshi with finding out Malcolm's favorite food in time for a surprise birthday dinner.

When the Enterprise comes in contact with an alien vessel transporting stargazers to observe a spectacular stellar event, Archer invites them aboard the ship not realizing that Silik, a Suliban enemy, is among them. Archer quickly realizes that Silik is engaged in a nefarious time-travelling mission and must stop him before he can tamper with the course of history.

The Enterprise crew is dispatched by Starfleet Command to assist Fortunate, a human freight vessel that has been attacked by Nausicaan pirates. On arriving, they are surprised to find that Fortunate's crew is resistant to Archer's efforts to help them and determined to seek revenge against their attackers, no matter the repercussions.

Captain Archer and the crew discover a fully inhabited, civilized though less advanced Earth-like planet. Disguised to look like its inhabitants, they pay the planet an exploratory visit where they learn that a pernicious illness is afflicting the local population. As Archer seeks to help them find the malady's source, he finds himself in a close encounter with a comely female alien.

A Vulcan starship interferes with Archer's probe of an oversized comet.