Excitement is brewing onboard Enterprise as the starship enters orbit of a Minshara-class planet with 500 million lifeforms. Visual and acoustic scans reveal a pre-industrial society called the Akaali. Over T'Pol's protestations of protocol, Captain Archer decides the crew should explore the civilization first-hand, rather than use probes. But the mission becomes more critical when neutrino emissions are detected on the surface, indicating an antimatter reactor on a world that doesn't even have indoor plumbing. So Archer sends himself, Ensign Sato, Commander Tucker and T'Pol down to the planet disguised as Akaali to investigate.
Split into two groups, the landing team follows their scanners through the night toward the telltale emissions. T'Pol and Sato are disturbed to see that many of the people on the streets of the city are afflicted with lesions. Archer and Tucker determine the antimatter reactor is located underneath a small curio shop, and upon breaking into the shop they find that the entrance to the reactor is protected by an energy barrier. Suddenly a crossbow is trained at them by a striking Akaali woman who accuses them of causing a local plague with their "evening deliveries."
T'Pol arrives and stuns the woman with her phase pistol. With dawn arriving, Archer sends the others back to the shuttle while he stays behind with the woman, whom he learns is an apothecary named Riann. When she wakes up, Archer tells her he's an investigator from another city who is as curious as she is about the strange goings-on at the curio shop and how they're related to the epidemic. When the shop opens, Archer and Tucker confront the owner, Garos, mutually realizing each are not of this world. Garos, a Malurian, claims to be an explorer like them who grew fond of the Akaali and chose to stay, and the antimatter reactor is nothing more than a fabrication device for food and clothing. He further claims the plague is caused by an indigenous virus, and Riann's accusations toward him are baseless. Archer is skeptical, so he visits Riaan in her lab with T'Pol. While T'Pol surreptitiously gathers data, Archer learns from Riaan that her brother was one of the first victims of the epidemic, which started shortly after Garos arrived. And suspicious deliveries are taking place at night from Garos' shop to different places outside the city. Later, Dr. Phlox determines from T'Pol's readings that the city's groundwater is contaminated with tetracyanate 622, a toxic compound primarily used as an industrial lubricant, which appears to be responsible for the plague.
That night Archer and Riaan watch the curio shop, waiting for one of those deliveries. Their stakeout turns awkwardly romantic when Archer's translator malfunctions and he has no choice but to kiss Riaan to cover while fixing it. But then they see a man hauling crates out of Garos' shop, and they follow him to a forest clearing. They watch as an alien shuttlecraft procures the crates with a tractor beam. Riaan is shaken by these sights, and Archer is about to confess his true identity when they come under attack by the delivery man. Archer fights with the attacker and succeeds in stunning him, in the process undoing his prosthetic disguise to reveal his scaly-gray alien skin. Archer pockets the alien's weapon, shop key and a remote control unit, then explains everything to Riaan as they return to the city. The enter the curio shop, use the remote to disable the energy barrier, and take a stairwell to find a massive underground drilling operation operated by scaly-gray aliens. Archer determines they're mining a veridium isotope, which is used to manufacture explosives, and their drill bits are saturated with tetracyanate. Determined to shut down the operation, Archer tells Tucker to use the transporter to beam out the reactor, once he can disengage the dampening field that envelopes the entire mine. But he and Riaan misread the alien controls and set off an alarm.
While a Malurian ship approaches Enterprise and opens fire, Garos confronts Archer in the mine and warns him to leave and never return. As Enterprise evades its assailant, Archer manages to disable the dampening field and escape with Riaan into the city where they get into a phase-pistol fight with the aliens in front of the shocked locals. Meanwhile Tucker tries to get a transporter lock on the reactor while Enterprise fails to fend off the Malurian ship. He gets the idea to beam the reactor into space and fire a spatial torpedo at it, creating an antimatter explosion that disables the attacking ship. On the ground, Riaan uses her scientific prowess and instructs Archer to shoot his phase-pistol into an oil lamp on the street above Garos and his henchmen, exploding it and thus giving Archer the upper hand. Defeated on each front, Garos and his men leave the planet. The Enterprise crew removes all the mining equipment and provides an antidote for the plague, all without the Akaali knowing what's really going on, with one exception: Riaan, who doubts anyone would believe her anyway. Archer shares one last kiss with her before trekking back into the unknown.