Sent by Admiral Forrest to respond to an automated distress call, Enterprise intercepts the Earth cargo freighter Fortunate and finds it badly damaged and not responding to hails. Captain Archer leads an away team to board the vessel, and they are greeted by the freighter's acting commander, first officer Matthew Ryan. Ryan informs Archer that the Fortunate was attacked by Nausicaan pirates, who have been harassing freighters in the sector for years, including the one Ensign Mayweather grew up on. Claiming the distress call was a mistake, Ryan resists Archer's overtures of help, but Dr. Phlox insists on tending to the injured captain. Once Phlox determines that Captain Keene will need two or three days of treatment, Archer talks Ryan into letting Enterprise engineers come aboard the Fortunate to upgrade its defenses. This forces Ryan and another crewman named Shaw to take special precautions to hide their secret — they have a Nausicaan prisoner on board whom they are torturing for information.
Later, a proud Mayweather gives Ryan a tour of the impressive new Enterprise. They bond as fellow "boomers" who both grew up on freighters, but Ryan proves to be disdainful toward Mayweather for having left his parents' cargo ship to join Starfleet. Meanwhile on the Fortunate, suspicious activity leads T'Pol to run scans and detect the bio-signs of an injured Nausicaan. Informed of this discovery, Archer confronts Ryan, who confesses they indeed are keeping a prisoner and argues they have every right to. Archer concurs, but counters that he also has a right to remove the improvements made on the freighter. Ryan appears to relent and let Archer and his team see the prisoner, but as he leads them into a cargo module, it proves to be double-cross — Ryan and Shaw trap them in the compartment with a breach in its hull, and detach it from the freighter.
The Fortunate then fires upon Enterprise and jumps to warp, escaping while Enterprise rescues the trapped crewmen. Commander Tucker sets out to the repair the damaged long-range sensors so Enterprise can track the renegade freighter, which they figure is after revenge against the Nausicaans. Mayweather approaches Archer and asks him to consider that maybe they should stay out of Ryan's way. But Archer argues that human beings have a code of behavior whether they're Starfleet officers or "space boomers," and Mayweather agrees. On the Fortunate, Ryan succeeds in beating the information he wants out of his prisoner, namely the shield frequency codes for the Nausicaan raider ships. They find the ship that attacked them and chase it to an asteroid where two other Nausicaan vessels are off-loading cargo to a docking station. Ryan orders an apprehensive Shaw to fire weapons, but their plasma bursts fail to penetrate the Nausicaan shields. A counterattack disables their engines and ability to escape, so the crew prepares to fight the Nausicaans face-to-face as they board the freighter to retrieve the captive.
Meanwhile, Enterprise has detected the Fortunate's weapons fire and sets course to intercept. As an intense firefight ensues on the Fortunate, Archer hails one of the Nausicaan captains to negotiate a peaceful solution, letting the freighter go in exchange for the hostage. Faced with the superior firepower of the NX-Class Enterprise, the Nausicaan captain agrees to let Archer deliver the prisoner, but he must be quick or he'll "take his chances" with an assault on both ships. Archer contacts Ryan and implores him to listen to reason. Ryan stubbornly refuses to give up his hostage, but then Mayweather speaks up and chastises Ryan for putting all freighter crews at risk to satisfy his thirst for revenge. When the Nausicaan ships start firing, Ryan finally gives in and releases the hostage to the boarding party, and the Nausicaan ships retreat. Ryan is later stripped of his rank by Captain Keene, and Keene confesses to Archer that it'll be hard for freighter crews to get used to seeing the space they've been traveling for three generations get a lot more crowded.