When militants take over a world, the Enterprise crew move to evacuate Denobulan geologists that are deep underground. Meanwhile, Phlox has to save a dying Antaran that refuses treatment due to the history of their races.

In a Klingon tribunal, Archer stands accused of aiding fugitives of the Empire and faces death if found guilty.

Noncorporeal aliens possess the bodies of the Enterprise crew.

Archer and Tucker are arrested and placed on a prisoner transport heading for a penal colony, Canamar. They won't have a chance to correct this error, as one of the inmates plots a takeover of the ship.

The Enterprise crew find a small craft drifting in space and are surprised to find it contains a human corpse. More questions arise when the Suliban and Tholians make claims to the craft.

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.

Enterprise visits a planet where an Interspecies Medical Exchange conference is being held. Dr. Phlox tries to obtain research on a terminal disease from the Vulcan contingency, without revealing T'Pol has been infected by it.

During a solo test mission on Shuttlepod One, Trip is attacked by a territorial alien and forced to land on the night side of a moon. As he tries contacting Enterprise, he discovers his alien foe has made an emergency landing nearby. The two contend with each other as an extremely hot sun rises and threatens both their lives.

When a lethal neutronic storm approaches faster than Enterprise can escape, the crew take shelter in the maintenance shafts inside the warp nacelles. They also provide refuge to a group of aliens, who aren't exactly honest about themselves.