Archer is contacted by Admiral Forrest to turn around and lend a helping hand to the ECS Fortunate, a Y-class freighter. Archer, Malcolm, Phlox, and Travis learn from the first officer that the Fortunate was attacked by Nausicaans and that the captain was injured. The Enterprise helps repair the Fortunate until sensors show that the 23-member crew has an additional person aboard.
An Earth freighter, the ECS Fortunate, with a crew of 23 is attacked by Nausicaans and the Enterprise is sent to investigate. When they arrive, the freighter is relatively unharmed apart from their captain, but the rest of the crew are secretive and reluctant to accept Enterprise's help. Initially they assume the self-sufficient nature of the "Boomers" is to blame. It transpires that the X.O. Matthew Ryan and his men are secretly torturing a captured Nausicaan for his shield access codes.
While helping repair the Fortunate, T'Pol detects the Nausicaan bio-sign. Ryan admits the Nausicaan is their prisoner and he is being interrogated for information on the pirates that attacked their ship and injured their captain. He refuses to hand over the prisoner or let Starfleet see him, until Archer threatens to take out all the spare parts they have installed on the Fortunate. Ryan reluctantly agrees to let Archer and his away team see the prisoner, but as they enter a cargo section of the freighter it turns out to be a trap. The cargo pod is jettisoned and breached by the "Boomers" with the away team inside. Before the Fortunate warps away to the Nausicaan base, it fires its plasma cannons at the Enterprise to delay pursuit. After the Enterprise recovers their people and repairs the long range scanners they pursue the freighter, tracking its warp signature.
Meanwhile, the Fortunate arrives at a hollowed-out asteroid the Nausicaans are using to off-load their stolen supplies. The crew of the Fortunate discovers that their shield codes are useless, and they are out-matched by the defending pirate vessels. Enterprise arrives and engages the Nausicaan ships, while the pirates attempt to board the freighter and rescue their captured crewman. Archer is able to broker a temporary truce: if he can return the Nausicaan captive, the boarding party will stand down. Ryan is uncooperative until Ensign Mayweather intervenes saying that Ryan's motivations are not about preventing future attacks on Earth ships; they are about his personal revenge. Mayweather asks what if the next ship that comes across the Nausicaans is his family's ship and it has to pay the price for what has happened here today? Grudgingly, Ryan agrees to stand down.
The recovered captain of the Fortunate and Archer have a conversation about Ryan's actions and his demotion to crewman 3rd class. The captains agree Ryan acted badly but the freighter skipper muses that acting on their own is all they've known for a century – citing it as the primary motivation his people are out here, to prove themselves. Archer reflects that more high warp Earth ships will soon be in their space "policing" the area and the freighter captain muses "things just won't be the same any more." Archer then declines a rare alien draught as a peace offering and the ships go their very separate ways.