They arrive at the planet and find no signs of life, but a metallic signature. Archer, T'Pol, Malcolm, and Hoshi go down to the planet, and they find a Xindi landing craft, where some charred, non-Xindi corpses are. They keep exploring, but then Malcolm turns into an alien who's behaving primally. T'Pol (whose temples have swollen but she's otherwise fine) goes back to the landing craft to find Archer having made the same transformation. She contacts Enterprise and calls for security, only for Archer to attack her (while speaking in an alien language). She stuns him, but Hoshi, who has also transformed, attacks her. T'Pol tries to run away, but falls over and is knocked unconscious.
The altered Archer, Malcolm, and Hoshi carry the unconscious T'Pol, tied up, and lay her down. She wakes up and asks to be untied, which Archer does, and she tries to use the universal translator. Meanwhile, on Enterprise, Phlox has found T'Pol's bio-sign. Trip, despite Phlox's warnings, decides to go down and search for the team, deciding to wear an EV suit.
T'Pol has gotten the universal translator up and running and has determined that the transmogrified crew members want to go to a place called Urquat to find the rest of "their people". She can't convince them to go back to the shuttle, so she decides to observe them for a while. At one point, they fight over some food that Malcolm picked from a tree.
Trip, Chang, and Palmer go down to rescue the away team, but Malcolm knocks out Chang and Hoshi chases away Palmer. Trip manages to stun Malcolm, but then Archer attacks him and cracks his helmet. T'Pol interrupts Archer and asks if he recognises Trip. Archer hesitates, but gets distracted by Palmer. T'Pol decides to stay behind with Archer and Hoshi, but tells Trip to take Malcolm back to Enterprise.
Phlox observes Malcolm in the decon chamber, where he finds out that the transformation is caused by a virus, but that T'Pol is immune because Vulcans have "K-cells", which are neutralising it. He thus concludes that T'Pol's DNA is the answer to the cure. Two alien ships then intercept Enteprise and declare them under quarantine.
They also want to board Enterprise, which Trip vetoes, but the alien commander, Tret, says that his people have studied the virus for sixty years and it must be "eradicated". Trip tries to point out that Malcolm's in isolation, and invites Tret onboard to discuss the situation but threatens a fight if he boards the ship by force. Meanwhile, on the planet, Archer dreams about reaching Urquat and gushes to Hoshi about it. T'Pol tries to tell them that Earth is their home, but they don't believe her.
Tret boards Enterprise and tells Phlox and Trip about the virus, revealing that it's very contagious and led to millions of his kind being killed to prevent spread. He also reveals that it was created by an alien race called the Loque'eque, who did it to propagate after going sterile, and it causes the infected to turn into Loque'eque and obsess over going home. Tret gets word from his ship that more infected are on the planet and orders a containment team together. Phlox reveals that T'Pol's immune, and wants to work with Tret, but Tret wants to work on his own and threatens to use force on Phlox if stopped. Trip then remembers that during the neuro-pressure session, T'Pol bit into a peach, and decides to get Phlox a DNA sample from there.
On the planet, Archer and Hoshi find Urquat, but it's in ruins. T'Pol suggests they go to Enterprise to find out what caused it, but Archer refuses, then starts to wonder if it was the Vulcans that destroyed Urquat. The containment team arrives, leading to a fight, during which Archer infects one of the aliens, who is subsequently killed. The aliens prepare to torch Archer and Hoshi, but then Trip and a MACO appear and stun them. Then, T'Pol finally convinces Archer to follow her back to the shuttlepod.
They go back to Enterprise, when the alien containment team starts firing at the ship. Tret hails them and orders them to drop out of warp. Trip begs them to give them time, and Tret refuses, until he sees Archer and Hoshi, who are partly cured. Finally realising that a cure is possible, the aliens call off their attack. Thus, they leave, giving the aliens some of Phlox's medicine to prevent further outbreaks.
Tropes in this episode include:
- Big Damn Heroes: Trip and another crewman beam down Just in Time to save Archer and Hoshi from being incinerated.
- Cassandra Truth: When T'Pol explains the situation to the transformed Archer, Malcolm, and Hoshi, they think she's lying.
- Chekhov's Gun: Trip gives T'Pol a Georgia peach early in the episode, apparently as an Apology Gift for canceling two prior neuropressure sessions. Later on, when Phlox needs a DNA sample from her, Trip retrieves the half-eaten peach.
- Dreaming of Things to Come: Transformed Archer dreams of finding the city Urquat, and sees it full of Loque'eque. Subverted when he reaches the city to find it destroyed, with no survivors.
- It's Probably Nothing: When Malcolm starts feeling uncomfortable on the planet, he figures it's just the tropical climate. This quickly becomes the least of his concerns.
- Kill It with Fire: How the unnamed aliens deal with anyone infected with the Loque'eque virus (they burn them to death), including one of their own people when his EV suit is breached.
- Last of His Kind: With the antivirus developed, Phlox's sample of the virus will eventually be all that is left of the Loque'eque. Archer knows it can't be set free, but does want it put in stasis rather than be destroyed.
- Recycled Plot: Something of a twist on Voyager's "Memorial."
- Sick Episode: Archer, Malcolm, and Hoshi end up catching a virus.
- Well-Intentioned Extremist:
- The alien commander. He wants to contain the virus and prevent anyone else from getting infected. However, his means include setting the infected on fire and destroying any vessel that might carry a creature with the virus.
- The Loque'eque as well. They just wanted to save themselves from extinction.