Eager to visit the deep-space colony of a race called the Paraagans, Captain Archer leads an away team toward the surface of an alien planet. While piloting the shuttlepod into the atmosphere, Reed proceeds cautiously as he follows the Paraagan landing protocols precisely, a necessity due to the high concentration of the volatile gas tetrazine at a certain altitude. He closes the shuttlepod's plasma vents as instructed (exhaust plasma being the only thing hot enough to ignite the tetrazine), but just then the shuttlepod is rocked by a deafening explosion, and a massive shockwave scorches the planet beneath them. After getting back to Enterprise safely, the distraught team learns the colony of 3600 people has been obliterated, and tries to figure out what happened. Reed is absolutely certain both plasma ducts were closed without malfunction, but Archer orders an investigation while he braces himself to report the incident to Admiral Forrest. While the crew continues its analysis and Archer deals with intense feelings of guilt, Forrest convenes an emergency meeting of the Command Council. He later informs Archer that Enterprise is to return home, and a Vulcan ship will rendezvous with them in three days to pick up T'Pol and Dr. Phlox.
The crew is despondent and frustrated not only that their own mission is cancelled but that Starfleet has been set back 10 or 20 years. T'Pol reports to Archer that Reed and his team have found an unidentified energy signature on the shuttlepod hull, but he dismisses the evidence as inconsequential. The captain climbs into bed after a very bad day, but when he calls for Porthos he gets no response. Turning the lights back on, he is bewildered to find himself in his apartment in San Francisco! Trying to figure out what's going on, he hears the com chirp, and receives a call from Tucker — the exact same call he remembers getting 10 months prior, the day before Klaang was found in the Broken Bow incident. A familiar voice in the room tells Archer he's not dreaming — and he turns to see Daniels, the time-travelling operative who was supposedly killed by the Suliban Silik. Daniels apologizes and explains that he needs to talk with him, and chose this time period to "hide" from certain factions involved in the Temporal Cold War. He further explains that the explosion at the Paraagan colony was historically not supposed to happen, that it was caused by someone who doesn't want Archer's mission to succeed.
Archer wakes up back in his quarters on Enterprise, his head now reeling with new information. First thing he does is get Reed to use a phase discriminator to expose an alien component that was attached to their shuttlepod, one designed to generate a plasma stream. Archer then orders his senior staff to create two quantum beacons with certain specifications, and to turn the ship back toward the Paraagan colony — he is now able to assure his crewmates that they weren't responsible for the accident. Archer has a specific plan, and it involves unlocking the quarters Daniels used when he was masquerading as a crewman, in order to retrieve a database containing schematics for a Suliban Stealth Cruiser.
Once they arrive at the planet, Archer then directs the ship to a binary system 2.5 light-years away, and then to a specific moon. The quantum beacons are deployed toward specific coordinates, and on the viewscreen the crew sees exposed a cloaked Suliban cruiser. They approach, and before the Suliban has a chance to fire weapons, Enterprise lets loose a barrage of fire from their phase-cannons and torpedoes, crippling their cloaking generator, weapons and engines. Archer, Tucker and T'Pol quickly take a shuttlepod to board the Suliban ship. Using stun grenades and other tactics to fight off the Suliban crewmen, the team finds their computer core, and Archer retrieves three data discs. With help from Reed's weapons on the starship, the team is able to make a harrowing escape. Once aboard, Archer has Mayweather immediately set course for the Vulcan ship they are to rendezvous with.
T'Pol and Hoshi are able to decode and translate the data disks, which reveal the Suliban were indeed responsible for the explosion that destroyed the Paraagans. Archer reports the finding to Forrest, who is baffled how he obtained this evidence but pleased he did, and tells him to proceed to the Vulcan ship as quickly as possible. Meanwhile at a Suliban helix hidden in a nebula, Silik reports the incident to the mysterious man from the future who controls the Cabal. The man orders Silik to bring him Archer, and must not fail. On Enterprise, Archer tries to explain his story to T'Pol, who refuses to believe it because the Vulcan Science Directorate has concluded that time travel is impossible. Just then the bridge crew notices an instability in the ship's warp field. Suspicious, Archer orders the quantum beacons deployed, and they discover they're surrounded by a swarm of cloaked Suliban cell-ships. They are hailed by Silik, who warns he has them easily outgunned, and demands that Archer give himself up to one of his ships. He gives Archer five minutes or he will destroy Enterprise. Caught in a corner, Archer puts T'Pol in command, asking her to be open-minded about things that may seem impossible, and glumly steps into the Turbolift to head for the docking port. When the Turbolift opens, he steps out into a decimated corridor — he is no longer on Enterprise! He is now in some alien building that has been utterly ravaged, with an eerie wind whistling through it.
Meanwhile Silik informs Enterprise that the captain's time is almost up — but there is no trace of Archer! So the whole swarm of Suliban ships prepares to destroy their warp core.
In the alien building, Archer finds himself at the edge of the bombed-out floor before a devastating vista, a once beautiful city transformed into a post-apocalyptic nightmare, burnt-out shells of skyscrapers spread out as far as the eye can see. Daniels is there, this time in his native clothing. Rattled like he's never been, Daniels says that he was just having breakfast there half an hour ago, then was instructed to bring Archer to his time — the 31st century — because the timeline wouldn't be safe if he boarded that Suliban ship. The sequence of events did not occur the way they were supposed to. Archer volunteers to go back and take his chances with Silik, to prevent this devastation from occurring, but Daniels reveals that all his equipment, including the time portals, have been destroyed. There's no way to send him back.