Silik and his Suliban soldiers board Enterprise to search the ship for Captain Archer, who T'Pol insists disappeared when he left to give himself up. Meanwhile, Archer is stuck in the 31st century with Daniels, trying to determine why his removal from the 22nd century led to the devastation they are witnessing. Daniels is stunned to discover that a monument commemorating an organization called the "Federation" was never built. The two find a dilapidated old library and begin searching for answers there. On Enterprise, the Suliban re-take the data disks stolen from them earlier showing they were the ones responsible for the catastrophe on Paraagan II. They also detect a temporal signature on board which proves T'Pol was not lying after all about Archer, so rather than killing the crew, Silik confines them to quarters and commandeers the ship. Meanwhile on Earth, Ambassador Soval is incensed that Enterprise has failed to follow instructions ending its mission, and tells Admiral Forrest he has no choice but to send the Vulcan ship D'kyr in pursuit.
Having docked Enterprise with a Suliban helix, Silik refuses to destroy it until he can contact his leader from the future for new instructions — because the temporal signature on Enterprise changes the whole scenario. Failing that, he prepares to interrogate T'Pol. In the 31st century library, Daniels reveals in vague terms that Archer was to have played a key role in the eventual formation of the "Federation," and he realizes that by removing him from his time, Daniels caused exactly what he was trying to prevent. Therefore Archer must be returned, but since all the time-portal equipment is gone, Daniels devises a plan that involves using parts from the captain's communicator and scanner. Silik drugs T'Pol and questions her about Archer, but though all her answers are truthful, they are of no help. Meanwhile the rest of the quarantined crew finds a way to communicate with each other through the door coms, and they begin plotting against the Suliban. A wobbly T'Pol is returned to her quarters, and while she tries to recuperate from the brutal interrogation she witnesses a blurry visual communication from Archer — he is calling from the future, and he has instructions.
Now that the crew is surreptitiously talking to each other, T'Pol informs them of Archer's message and they set out to execute a scheme to get by the Suliban and retrieve a piece of futuristic equipment from Daniels' former quarters on the ship. Lt. Reed finds the device in a dimensional "hole" in the wall, but he is immediately captured by the Suliban and beaten for information. Reed tells Silik that he doesn't know what the device does, but was instructed by Archer, before he left, to destroy it so Silik wouldn't find it and use it "to contact someone." This leads Silik to believe the device will help him get in touch with his leader. As Silik returns to his temporal chamber on the helix with the device, Trip Tucker and T'Pol take back control of Engineering and set into motion an apparent reactor breach. Hearing the news of the impending explosion, Silik orders the Suliban forces to evacuate the ship and tow Enterprise away from the helix. They do so, and the Suliban cellships clear out as it appears Enterprise is about to blow up. But then the starship jumps to warp — it was all a fake pyrotechnic display. But the Suliban are quickly on to them and pursue. Meanwhile Silik is trying to tune the futuristic device and contact his boss. A figure slowly takes shape in a column of light, but then to Silik's surprise the figure leaps out and tackles him — it's Captain Archer!
Holding a weapon to Silik's temple, Archer demands the data disks back and takes him hostage as he leaves the temporal chamber, destroying the futuristic device on the way. Meanwhile Enterprise is engaged in a firefight with dozens of Suliban cellships, and just when it seems defeat is imminent, the Suliban suddenly stand down and peel away. One final cellship approaches — manned by Archer, back from the future, with an unconscious Silik in tow.
After rendezvousing with the D'kyr, Archer presents the evidence regarding the Paraagan tragedy, and Enterprise is vindicated. Despite that, Soval announces his intention to recommend the recall of Enterprise based on its "reckless" first year in space. Archer finds himself pleading for reconsideration, but then T'Pol steps in and points out in an almost impassioned speech that Vulcans were once very much like the humans now. Apparently she put it over the top, as the decision is made that the Enterprise mission will continue.