In scanning the Xindi database obtained from the marauder ship, Captain Archer manages to discern that the Xindi recently visited a nearby planet, and plans to see if it will provide any more clues regarding the mysterious species.
Once there, Archer, T'Pol, Hoshi and Reed head down to explore the jungle-like world. They discover a Xindi landing pod, which appears to be damaged by weapons fire. They also find some alien remains, though they don't appear to be Xindi. As the four officers continue to explore, strange changes begin to take place. T'Pol, separated from the others, notices that she is developing bizarre alien characteristics. She goes in search of the others, and finds that they have completely mutated into alien beings — they don't seem to recognize her and are speaking in a strange language. T'Pol manages to communicate briefly with Enterprise, but is soon taken hostage by her altered colleagues.
T'Pol nabs Hoshi's universal translator and uses it to communicate with the others. The alien Archer, Reed and Hoshi all seem intent on returning to their homeland, which they call Urquat. T'Pol tries to convince them to return to Enterprise, but the beings do not trust her and insist on trekking through the jungle.
Back on Enterprise, Trip decides to take action and heads down to the surface with two MACOs. They manage to capture the altered Reed, but one of the MACOs is injured. Archer and Hoshi retreat to the jungle, so T'Pol decides to stay with them while Trip takes Reed to the ship. Back on Enterprise, Phlox studies the alien Reed and deduces that the officers have contracted a mutagenic virus, which was apparently designed to rewrite the DNA of its host. In other words, it will change the humanoids it infects into another species. The virus has little effect on Vulcans, which explains why T'Pol remained mostly the same. Therefore, Phlox wants to concoct an antivirus using T'Pol's genetic profile.
Before Trip can ponder this much further, Enterprise is hailed by a pair of alien vessels. Their leader, Tret, says that they have detected a dangerous virus onboard Enterprise — the ship must be quarantined and the carrier of the virus must be destroyed. As this would mean killing Reed, Trip refuses. Tret comes onboard to discuss the matter further, explaining that this particular virus infected tens of millions of people on his homeworld. If they hadn't destroyed these people, the virus would have transformed the entire population into an alien race. Tret goes on to explain the origins of the virus — it was created by the former inhabitants of the planet, the Loque'eque. Centuries ago, they lost the ability to reproduce and created the virus to transform other species into their own in order to save themselves from extinction. Tret is concerned that, if those infected leave the planet, the virus will be spread to other systems, resulting in an epidemic. Upon learning that there are other infected beings on the planet — Archer and Hoshi — Tret prepares to send his men down to eradicate them.
Down on the Loque'eque planet, Archer has a dream about Urquat. With renewed passion, he attempts to find this place, claiming that it is underground. He leads T'Pol and the alien Hoshi to some underground tunnels ... but once they reach what is supposed to be Urquat, all they find is ruins, a devastated civilization that obviously hasn't been inhabited for many years. Suddenly, they hear Tret's men approaching. They manage to escape to the surface, but more of Tret's officers are waiting for them. Luckily, Trip and the MACOs arrive just in time to save them, and take them back to Enterprise. Phlox has managed to synthesize an antidote to the virus using T'Pol's DNA. As he prepares to cure the altered crewmembers, Enterprise takes off with Tret's ships in hot pursuit.
Tret's ships fire on Enterprise, but before they can do any serious damage, Phlox presents a now-human Archer and Hoshi, proving that he was able to find a cure for the virus. Archer agrees to give Tret some of Phlox's serum in order to prevent future outbreaks. Phlox suggests destroying the last of the virus, but Archer insists they keep it onhand. He explains that he believes Tret's men will most likely wipe out all trace of the virus. As it was created in an effort to preserve a civilization, Archer believes it's best to save what remains of this species.