Six weeks into the Delphic Expanse, Captain Archer and his crew are still searching for clues regarding the mysterious Xindi. They're also adjusting to the newest members of the crew, a squad of Military Assault Command Operation soldiers (MACOs), led by Major Hayes. The crew learns of a Xindi working at a mining complex, and set out to track him down. Once they reach the complex, Archer and Reed head down to the grimy mine and meet with the alien Foreman. The Foreman offers a severed finger that he claims belongs to the Xindi worker. In exchange for a meeting with the worker, the Foreman demands a half liter of liquefied platinum. Back onboard, Phlox analyzes the finger and confirms that it is from a Xindi — however, it bears some intriguing variations from the Xindi corpse that was recovered on Earth. The corpse, Phlox explains, was reptilian. The finger is not.
Meanwhile, Trip labors to strip some of Enterprise's antimatter relays in order to provide the Foreman with his liquefied platinum. Trip and Archer return to the mining complex and, in exchange for the platinum, are introduced to Kessick, a humanoid Xindi. Archer asks Kessick for the coordinates to the Xindi homeworld, but Kessick refuses to give them up. He will only share this information, he says, if Archer helps him escape from the mining complex. As they are arguing, T'Pol contacts Archer and informs him that there are three warships approaching Enterprise at warp. Archer orders her to go to tactical alert and plans to return to the ship. Realizing that Archer has a starship in orbit, Kessick informs him that he's walked right into the Foreman's trap — the Foreman plans to add the Enterprise crew to his labor force. Kessick says that he can get Trip and Archer to their shuttlepod on the surface, but they will need to take him with them. Seeing no other alternative, Archer agrees.
Back on Enterprise, T'Pol is contacted by the Foreman, who informs him that Archer and Trip have been delayed. Suspicious, T'Pol orders Reed to devise a plan to recover the two officers, and to have Major Hayes assist him. Hayes and Reed clash, however, when the major suggests that Reed's team is too valuable to put in the line of fire, and that the MACOs should handle the mission instead. Reed is irritated, but finally agrees. Still, he insists on leading the mission himself.
Meanwhile, Kessick leads Archer and Reed through a sewage tunnel to a plasma duct. As the three men climb through the plasma duct, the Xindi reveals more about his people, telling Archer that there are five distinct species, all in conflict with one another. Unfortunately, the Foreman is wise to Archer's escape attempt, and orders the plasma re-routed through the duct. Archer, Trip and Kessick struggle to reach the closest maintenance hatch — but once they do, the guards are waiting for them. Kessick tries to pretend that he is an innocent prisoner of Archer, but the guards drag all three men to the Foreman, who orders them killed. Suddenly, Reed and the MACOs burst onto the scene, intent on rescuing Archer and Trip. An intense fire fight ensues, and Kessick is hit and knocked unconscious. Everyone manages to make it back to the shuttlepods and return safely to Enterprise. Just as the warships are about to catch up with it, Enterprise jumps to warp. With everyone back onboard, Phlox attempts to treat the wounded Kessick, but the Xindi is badly hurt and dies. With his dying breath, he gives Phlox the Xindi homeworld coordinates to pass on to Archer.
Meanwhile, Trip is having trouble sleeping, and has been having recurring nightmares about the death of his sister. Phlox recommends that T'Pol try treating the commander with Vulcan neuro-pressure, a somewhat intimate method that is supposed to be highly effective. After much urging, Trip finally submits to the treatment, and is surprised to find that it works very well.
Unbeknownst to the crew, the Xindi council is monitoring their actions and some factions believe that Enterprise is only the first ship of an Earth invasion. The Xindi-Insectoids wants to destroy Enterprise, but the Xindi-Humanoids believes that it is best to keep hidden until the new weapon is complete. Also locked in conflict are the other factions of the species: Xindi-Sloths, Xindi-Reptilians and Xindi-Aquatics.
Once Enterprise reaches the coordinates of the Xindi homeworld, the crew is surprised to find that there is only a large field of debris — the remains of a planet. The world has been gone for over a hundred years. T'Pol deduces that the new weapon must be being developed in the same location as the probe that attacked Earth. Considering this, Archer orders Mayweather to take them deeper into the Expanse.