After returning from an exploratory away mission to a pre-warp society on the brink of war, Lieutenant Reed is unable to locate his communicator. A search of the shuttle bay area proves fruitless, so Captain Archer and Reed return to the planet to try to find it, so as not to leave a contaminant within the culture. Unfortunately, they then manage to walk into a trap set by the local military, who have already found the communicator. With their capture, the local commander, General Gosis, also possesses 'contaminant' scanners and a phase pistol as well.
Becoming desperate to locate the away team, Sub-Commander T'Pol's attempt at contact actually divulges the Captain's identity, and Archer and Reed are physically interrogated. After a mild beating, it is discovered that not only are Archer’s and Reed's forehead morphology not the same as the locals', but they also have iron-based red blood, and vastly different internal organs. In response, Archer and Reed improvise a story about being genetically-altered prototypes (with prototype equipment) from an opposing faction known as the Alliance. While allaying suspicion that they are aliens, the military commander decides to hang Archer and Reed so that autopsies can be performed to discover more about their "enhancements".
Meanwhile, on Enterprise, a rescue mission is planned by Commander Tucker using the captured Suliban cell ship (as seen in episode Broken Bow), but problems arise with its cloak. In their cell, Archer and Reed contemplate the irony of their adherence to an early version of Starfleet'sPrime Directive. As they are about to be hanged, the cloaked Suliban ship with T'Pol, Tucker, and Ensign Mayweather arrives, enabling Archer and Reed to escape with their shuttle-pod and captured technology. Later, back on Enterprise, Archer reflects on the consequences of their actions even in the absence of foreign artifacts, and T'Pol is impressed that Archer was willing to sacrifice himself in the line of duty.