On a tip from Hoshi's telepathic admirer, Tarquin, Archer and the crew head to a nearby planet, hoping to learn more about the mysterious Xindi weapon. Archer, Reed and Major Hayes embark on a reconnaissance mission and discover that the sparsely-populated planet is home to an elaborate Xindi-Sloth manufacturing plant producing canisters of a substance called kemocite. The team manages to swipe one of the canisters, which is then transported onboard Enterprise for analysis. Unbeknownst to the Enterprise crew, Degra, one of the Xindi-Humanoids, is close to testing the weapon and needs only one more shipment of kemocite to do so.
Archer and the others manage to track down Gralik, the Xindi-Sloth in charge of the plant. Gralik answers Archer's questions about kemocite, but claims not to know about the Xindi weapon. Meanwhile, T'Pol has identified the imprint on the canister — it matches the signature of the Xindi probe that attacked Earth. Also, Trip has found the same imprint on a Xindi-Reptilian rifle and asks permission to take it apart for further investigation. Archer agrees and tells Reed to prepare to destroy the kemocite plant.
Archer confronts Gralik again, this time showing him the fragment of the Xindi probe and explaining that it killed seven million people on Earth. Upon examining the probe further, Gralik notes that the kemocite used in the probe definitely came from his facility. Sadly, Gralik realizes that Archer is telling the truth — Degra is using the current shipments of kemocite to build a larger, more deadly weapon. He reveals to Archer that there used to be a sixth species of Xindi — the Avians — but they were killed off during the same war that destroyed the Xindi homeworld. The other five species are scattered across the Expanse. Most of them, says Gralik, live peaceful lives — but obviously not all.
Meanwhile, on Enterprise, Trip and Phlox run tests on the Xindi rifle. Trip's scans show that the rifle has organic compounds — a pair of worm-like components with reproductive capabilities. Phlox notes that the worms' neural pathways modulate the rifle's power — an extremely sophisticated example of bio-mechanical engineering. Phlox attempts to break down the creatures' immune systems, eventually succeeding by using delta radiation. Trip notes that portable EM emitters might be able to knock out these Xindi rifles, giving the crew better defensive capabilities in the event of an attack. Trip and Phlox decide to test this theory out, even though T'Pol cautions that it might be dangerous. When they attempt to fire the weapon, however, it begins overloading and triggers a countdown — it's booby-trapped. Luckily, Trip manages to transport the rifle off the ship before it explodes.
Back on the planet, T'Pol alerts Archer to an approaching vessel. It's the Xindi-Reptilian ship that previously attacked Enterprise. Degra and his Reptilian cohorts have arrived ahead of schedule for their shipment of kemocite. Gralik offers to speak with Degra and obtain information for Archer — he's upset that his work is being used to build such destructive weapons. Archer, however, isn't sure if he can trust Gralik. In the meantime, Degra and the others have noticed that Gralik is missing, and send bio-mechanical drones known as Seekers to search for him. After out-running the Seekers, Archer and the others take cover in some nearby caves. Archer tells Gralik that he doesn't wish to harm the people of the colony, who had nothing to do with the attack on Earth. The captain finally decides he can trust Gralik, and devises a plan.
While Gralik stalls for time by running more tests on the kemocite shipment, Archer has the canister of kemocite that was sent up to Enterprise beamed back down to the planet. He then sneaks into the Xindi shuttle and replaces one of the canisters onboard with the one from Enterprise. Now, Enterprise will be able to track the canister ... and the Xindi.
After Degra leaves, Archer visits Gralik to say good-bye, and warns that Degra will eventually discover that the kemocite was sabotaged. Gralik, however, only hopes that he has delayed progress on the weapon and wishes Archer success in the mission. He also hopes that the captain will remember that not all Xindi are the enemy.