After returning from an exploratory away mission to a pre-nuclear fission era society on the brink of war, Lt. Reed discovers that he 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, instead of locating the device, they manage to walk into a trap set by the local military, who have already found the communicator. With their capture, the local authorities also have scanners and a phase pistol as well.
Becoming more 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. A physical examination reveals that they also have vastly different internal organs. In response to the escalating situation, Archer and Reed improvise a story about being genetically-altered prototypes (with unique 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 Chief Engineer Tucker. They plan to use the captured Suliban cell ship under cloak to mount the rescue of the prisoners at the detention center. However, while trying to get the cloak to work, Tucker's arm is accidentally irradiated and rendered invisible. With the execution imminent, a rescue attempt must proceeed, cloak ready or not, through the enemy's airspace.
In their cell, Archer and Reed contemplate the irony of how it is better that they sacrifice themselves to preserve their identities, rather than doing any more damage to the local culture. As they are about to be hanged, the Suliban ship with T'Pol, Tucker, and Mayweather arrives cloaked, interrupting the execution, enabling Archer and Reed to escape and retrieve their captured technology and parked shuttle-pod. Later, back on Enterprise, Archer reflects on the consequences of the events on the planet even in the absence of foreign artifacts. T'Pol is impressed that Archer was willing to sacrifice himself in the line of duty, since it was more than she expected of him.