Plot

His memory crippled, Archer awakens years in the future, after the Xindi have reduced Earth to a cinder and the remnants of humanity have settled on a distant planet. Now, Archer learns that he may be the key to undoing this tragedy.

Enterprise is hit with a rather intense anomaly. Refusing to leave an injured T'Pol behind, Archer is struck by the anomaly, leaving his brain infected with parasites, preventing him from making any new memories. Fast-forward 12 years. T'Pol has been caring for Archer since his affliction. As she does every day, T'Pol catches Archer up on the past 12 years, knowing he will forget everything within hours. She was in command of Enterprise after his injury, that the parasites live outside normal space-time and usual remedies never worked, that the Xindi were successful, and managed to destroy Earth and kill all but 6,000 humans. But today is special; Dr. Phlox is ready to give Archer the treatment he has been developing for ten years, which must be performed on Enterprise.—Meribor

While rescuing Sub-Commander T'Pol from a spatial anomaly, Captain Archer is infected by subspace parasites in his cerebral cortex, resulting in Anterograde amnesia. His condition prevents him from forming new long-term memories. This allows him to remember everything prior to the accident, but any new memories fade within a few hours. It soon becomes clear that Archer is not fit for duty (He is consistently forgetting things and Phlox is not able to find a cure in the short term, although he promises to continue working on it, till he does), and he is subsequently relieved of his command by Admiral Forrest (who had called T'Pol directly). T'Pol is granted a field commission to Captain, but the mission (To stop the Xindi weapon from reaching Earth) (T'Pol manages to find the location of the weapon, but is attacked by the reptilian ships. T'Pol rams the 2 reptilian ships into each other (when one of them docks with the Enterprise), but in the process kills 13 crew and damages the warp nacelle. Tucker says he can give a max of warp 1.7 with the 1 remaining nacelle) (Tucker is not happy that the mission is getting worse since T'Pol took command) fails and Earth, alongside every other human colony, is destroyed by the Xindi weapon. The few surviving humans (less than 6000) form a convoy, led by the Enterprise, which travels to the planet Ceti Alpha V. Admiral Soval (Gary Graham) offers T'Pol to return to Vulcan, but she refuses.

Twelve years pass and Archer, still plagued by memory loss, lives with T'Pol in a house on the colony. She has given up her career to care for him. They are visited by Doctor Phlox, who eventually engineers a cure for the parasite on Denobula (he takes Archer to the Enterprise to test his cure). He also discovers that when the subspace radiation treatments kill one of the parasite clusters in Archer's brain, it also vanishes from every other previous medical scan - as if the parasite had never existed. Therefore, since Archer will never have been infected, he would have remained Captain and possibly prevented the chain of events that led to Earth's destruction.

Unfortunately, the ship, now captained by Captain Tucker (and patrolling the Ceti Alpha system), is observed and attacked by Xindi vessels before the treatments can be completed. The Xindi were following Dr Phlox and wanted to prevent him from completing his cure on Archer. Apparently they knew that destroying the parasite in the present, can alter the past. The Enterprise is outnumbered and heavily damaged, the bridge is destroyed. Phlox, T'Pol, and Archer race to create a subspace implosion and as their procedure nears completion, Phlox, T'Pol and the entire bridge crew are killed. Archer himself is fatally wounded but manages to complete procedure. The ship is destroyed, but their plan works and the subspace parasites are also destroyed by the implosion, and wiped out through time. The time-line is reset; Archer is in sickbay recovering from a physical injury but will never develop the amnesia he originally suffered.