Archer, Malcolm, and Hoshi return from an away mission in a pre-warp culture. In decon, however, Malcolm realises that he's lost his communicator! They search the room, the launch bay, and the shuttlepod, but it's not there, meaning that he must have left it behind. Hoshi does a scan, and they find where on the planet the communicator is, so Archer and Malcolm must go down and retrieve it.
At a bar they went to before, the bartender secretly tells three other aliens that the humans are suspicious, and Malcolm finds his communicator. They go to the room where it's being kept, but it's locked, and the three aliens attack the two men and bring them into the back room. There, they find out that the aliens are local military, who lured the humans there for questioning. Their leader, Pell, orders a message to a general named Gosis in the belief that he has found two spies for an enemy faction known as the "Alliance".
Back on the ship, Trip believes that something is wrong, and T'Pol, despite acknowledging that it risks them being detected, hails them. They don't reply, and Hoshi finds that they are not at the bar. T'Pol orders her to keep scanning for them.
Meanwhile, Archer and Malcolm are in a detention centre and Malcolm wonders if he should tell the truth, since their false belief is dangerous. The man they met before arrives to bring them to be interrogated by Gosis, having heard T'Pol's hail, and asks which of the two is the "captain". Archer replies that he is, but that they're not military. During the interrogation, Gosis suggests that they're assassins and hits Archer on the head twice. Upon discovering that Archer's blood is red, Gosis orders that he and Malcolm be examined by a doctor named Temec.
Back on the Enterprise, Hoshi finds Archer and Malcolm and she and the others hatch a plan to rescue them. Trip decides to use a Suliban cell ship to rescue them, but while trying to get the cloaking device going, he accidentally cloaks his forearm. Phlox can't scan Trip through the cloak, but thinks that he will most likely be fine, and gives him a glove.
On the planet, Gosis has now found out that the humans' organs are different from his own, and the aliens' surveillance has captured a picture of the shuttle travelling very quickly. The humans lie that they are genetically engineered spies who are equipped with prototype technology. Gosis doesn't believe them and sends them back to the cell, but Temec believes them and considers killing and dissecting them.
T'Pol suggests Trip finish his work on the cloaking device on the way to the planet, and meanwhile, Archer and Malcolm anticipate dying. They wonder if they should tell the truth, but Archer eventually decides that'd be a bad idea even if it saved their lives.
T'Pol, Trip, and Travis launch and are intercepted by three aircraft. They transfer the power to the weapons, but that makes the warp fail. While Trip fixes the problem, Archer and Malcolm get taken to be executed (specifically by hanging). Archer tries to plead for Malcolm's life, but Gosis doesn't respond. Thankfully, Trip, T'Pol, and Travis arrive just as the nooses get tied and they save the day. They retrieve their equipment and take off in the shuttle, with a confused Gosis watching.
Back on Enterprise, the crew discuss what happened, concluding that they caused a bit of cultural contamination in that the aliens now believe their enemies are more technologically advanced than they really are. On the plus side, however, T'Pol is impressed with Archer being selfless enough to sacrifice his life to protect the aliens.
Tropes in this episode include:
- Alien Blood: Implied but not seen, given the aliens are shocked at the humans having red blood. For them, iron (an essential component of hemoglobin) is toxic.
- Alien Non-Interference Clause: Discussed. Archer and Malcolm are willing to give their lives to prevent any further contamination.
- An Arm and a Leg: Their attempt to get the Suliban cloaking device ends up cloaking Trip's right arm. It eventually decloaks, of course.
- Big Damn Heroes: Trip, T'Pol, and Travis arrive to save Archer and Malcolm just moments before they're about to be hanged.
- Bittersweet Ending: The crew contaminated the aliens' culture, but they got their technology back, escaped execution, and T'Pol is impressed with how noble Archer behaved.
- Bizarre Alien Biology: A rare inversion, showing how bizarre human biology is from the aliens' point of view.
- Call-Forward: At the end of the TOS episode "A Piece of the Action", Kirk remonstrates Bones for leaving his communicator behind. This episode shows why it's such a big deal.
- Distressed Dude: Both Archer and Malcolm end up being imprisoned and nearly killed, requiring Trip, T'Pol, and Travis to save them.
- Gone Horribly Right: Temec believes Archer and Malcolm's lie that they're genetically engineered spies, but it makes him want to dissect them.
- Nice Job Breaking It, Hero: After extensive tests, the military see how different human physiology is, and they're perfectly willing to entertain the idea that they're aliens. Their major concern is if they're helping "the Alliance." However, Archer and Malcolm are able to convince them that they're actually genetically-engineered Super Soldiers, armed with prototype particle weapons. Their rescue comes in the form of the Suliban cell ship, which remains cloaked (mostly). Needless to say, Archer is not happy after the mission.
- Oh, Crap!: Malcolm starting to frantically go through his pockets, realizing he lost his communicator.
- Schizo Tech: Downplayed. Archer mentions that the aliens haven't yet developed atomic power. We don't see any evidence that they have technology substantially more advanced than Earth did prior to nuclear power, but they find it plausible that another nation has developed handheld energy weapons and advanced genetic engineering.
- Take Me Instead: Archer tries to convince General Gosis to only execute him, as Malcolm is his tactical officer and has "useful information about the Alliance."
- What Happened to the Mouse?: The Suliban cell ship they captured in "Broken Bow" is finally brought up again, and is promptly forgotten again.
