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Upon returning from a research mission to a pre-warp alien planet, Reed discovers that his communicator is missing. After an extensive search, he realizes that he must have lost it somewhere on the planet. Hoshi manages to tap into the communicator's power signature and pinpoints its location near a tavern that Reed and the rest of the team visited. Archer knows that the crew must retrieve their technology or risk contaminating the planet's pre-warp society, so Archer and Reed return to the planet, hiding their shuttlepod in the woods. As they enter the tavern, a group of soldiers eyes them suspiciously. Using his scanner, Reed realizes that the communicator is located in another room of the tavern, but when he and Archer go to retrieve it, they are apprehended by the soldiers. The two men are taken to the tavern stockroom and questioned by Major Pell, who asks if the communicator is a weapon. Pell also seems to think Archer and Reed are connected to something called "the Alliance." When the men refuse to respond, Pell orders that they be taken to the military complex.

At the complex, Archer and Reed are interrogated by Pell's superior, General Gosis. Gosis informs them that someone named "T'Pol" was trying to reach the "captain" via the communicator. Archer identifies himself as the "captain," which only furthers Gosis' suspicions that the two men are military recruits for the Alliance. During the interrogation, part of Archer's alien prosthetic comes off, revealing his human face. Gosis doesn't know what to make of this, and orders a full medical examination.

Meanwhile, on Enterprise, Hoshi has managed to locate Archer and Reed, and Trip suggests taking Shuttlepod Two to rescue them. T'Pol, however, is reluctant to risk further contamination of the pre-warp culture. So, Trip comes up with another idea. As Enterprise is still in possession of the Suliban cell-ship, perhaps he could attempt to bring its cloaking device online — the crew would be able to rescue their missing crewmen without being detected. T'Pol agrees, and Trip and Mayweather begin work on the cell-ship. As they work, Trip is somehow affected by the particle radiation the ship uses to conceal itself rendering his right arm invisible! Phlox guesses that it will eventually materialize on its own, and gives Trip a surgical glove to use in the meantime.

Back on the planet, Gosis is astonished at the results of the medical tests. He can find no reasonable explanation for the various physical "deformities" displayed by Archer and Reed, and continues to press them for answers. Unfortunately, Gosis has yet another suspicious piece of evidence — a surveillance photo of the Enterprise shuttlepod. As it appears he may be getting closer to the truth, Archer offers an explanation: he and Reed are prototypes for a genetically-enhanced Alliance super-soldier, and the various pieces of technology they have with them are Alliance prototypes as well. Gosis believes this might be a logical explanation, but he needs proof — so he orders the execution of the two men. Once they're dead, the doctor will be able to study their organs in more detail.

On Enterprise, Hoshi manages to intercept a message saying that two "enemy spies" are set to be executed. With time running out, T'Pol, Trip and Mayweather head down to the planet in the cell-ship, which still isn't cloaking properly. Meanwhile, Archer and Reed prepare to face their execution, determined to sacrifice their own lives rather than contaminate this alien culture. As they are led to the gallows, Trip and the others struggle to get the cell-ship cloaked in the air. They are pursued by military aircraft, but the ship cloaks at the last second, and they manage to land at the site of the complex just in time to save Archer and Reed. Archer retrieves Enterprise's technology, and the crewmembers pile into the still-cloaked cell-ship just in time.

Once onboard, Archer thanks T'Pol for taking a risk to save his life. She notes that even though they managed to retrieve the technology, they have contaminated a pre-warp culture. Still, she's impressed that the captain was willing to sacrifice his life to protect an entire alien race. As for Trip, his arm has rematerialized and is visible again ... for the most part.