After visiting the research site, Admiral Forrest calls in Enterprise to find the transport. On the way, the crew receives a distress call from a Tarkalean freighter, which is under attack from an unknown species. Once they track down the freighter, the crew notes that it is being attacked by a modified version of the arctic transport.

Enterprise fends off the transport and brings the two Tarkalean survivors onboard. Phlox notes that they should live, but that nanoprobes from this cybernetic species have infiltrated their systems. They are being transformed into a cybernetic hybrid, and the formerly human researchers are most likely going through a similar transformation. Phlox is attempting to come up with something that will slow the nanoprobes' progress. Though Phlox doesn't believes these beings are a danger to the crew, Archer orders Reed to post a guard in Sickbay.

As Enterprise continues to search for the transport, Archer realizes that there's something familiar about this incident. He points to a speech Zefram Cochrane made years ago, wherein Cochrane referred to "cybernetic creatures from the future." T'Pol is skeptical of Cochrane's comments, but Archer remains troubled — Cochrane said that the creatures' ultimate goal was to "enslave the human race."

Back in Sickbay, Phlox is attacked by one of the cybernetic beings, who injects him with some strange tubules. The two altered Tarkaleans also attack the security guard and escape. When Phlox comes to, he realizes that he's been infected with nanoprobes. While he works furiously to figure out a treatment, Archer orders Reed and his security contingent to scour the ship for the altered Tarkaleans. As they search, the beings manage to modify most of Enterprise's primary systems. When Reed finally tracks them down, phase-pistols seem to have no effect on them — in fact, they're able to adapt very quickly and shield themselves from weapons fire. Desperate, Archer is forced to seal the modified Tarkaleans off from the rest of the ship and eject them into space.

Soon, Enterprise manages to locate the transport and sets out after it. While Trip and Reed prepare for the inevitable encounter with the strange beings, Archer and T'Pol wonder if they'll be able to save the now-altered humans aboard the transport. Meanwhile, Phlox has figured out a way to reverse his transformation — he will need to subject himself to an intense dose of radiation. If the procedure should fail, he warns Archer, the captain will have to end Phlox's life.

The crew finally tracks down the altered transport, which has increased in size. The transport targets the modified systems on Enterprise, effectively shutting the ship down. An incoming transmission informs the crew that they will be assimilated — resistance is futile. But Archer isn't ready to give up just yet. He and Reed transport over to the ship, determined to shut it down. While there, they encounter the now-altered arctic researchers, as well as other cybernetic lifeforms that used to be human. Reed and Archer head for the ship's EPS manifold, fighting off these lifeforms all the way. They manage to attach several charges to the manifold, then transport back to Enterprise. Once they do, the charges explode, ripping through the vessel. Still, Reed notes that the systems on the transport are quickly restoring themselves. With Enterprise's weapons coming back on-line, Archer orders Reed to target the transport's warp core. Enterprise fires, and the transport explodes.

Meanwhile, Phlox has managed to cure himself using the radiation. His experience has left him somewhat unsettled, however. He tells Archer and T'Pol that while he was infected, he seemed to have a connection with the rest of the aliens, as if he was part of a collective consciousness. They seemed to be trying to send some sort of message. As Archer later deduces, the message was actually a set of coordinates — the creatures were telling their homeworld how to find Earth. Though the danger seems to have passed for the time being, Archer worries that he's only postponed the inevitable invasion...