(covers information from several alternate timelines)
In 2153, while chasing the Xindi weapon, Captain Jonathan Archer was infected with interspatial parasites while trying to save the life of T'Pol. As a result of the amnesia the parasites induce, Archer was rendered incapable of commanding Enterprise NX-01 and the Xindi destroyed the Earth in 2154. The remnants of humanity, around 6,000 people, eventually settled on Ceti Alpha V while the Xindi hunted the galaxy for them.
Determined to cure Archer, Doctor Phlox spent the next twelve years searching for a way. After learning that the only existing way to destroy the parasites would be to vaporize Archer in a subspace implosion, Phlox worked on developing his own treatment and came up with an antiproton beam powered by the Enterprise's warp core. The first use of the beam eliminated one of three clusters of the parasites in Archer's head in both the present and on all of the previous scans taken by Phlox. Phlox and T'Pol come to realized that if they eliminated all of the parasites in the present, they would be eliminated in the past too, potentially altering the timeline for the better as Archer would never have been infected and could conceivably lead the Enterprise to victory over the Xindi.
Before the treatments could resume, the Enterprise captured a Yridian spy who had informed the Xindi of the location of the remnants of humanity. Needing all power for the weapons, Captain Tucker ended the treatments and shortly afterwards, six Xindi ships were detected entering the system. (ENT: "Twilight")
Enterprise NX-01 engaged the six Xindi ships with phase cannons. Though the ships returned fire, the new shields, provided by General Thy'lek Shran held. The Enterprise broke off and was followed by an Insectoid and a Reptilian ship while the rest headed for the planet. As the two ships chased the Enterprise, they were attacked from behind by the Intrepid and another starship, disabling the Insectoid ship. The Enterprise then focused its fire on the Reptilian ship, knocking out its engines. The defeat of their two ships caused the four remaining Xindi ships to alter course to engage the three defenders.
Under heavy attack, the Enterprise managed to destroy an Insectoid ship, but started taking damage itself with forward shielding going down to 52%. An Insectoid and Reptilian ship targeted the Intrepid together, blasting off its port nacelle. With no other choice, Trip ordered them to retreat. The Enterprise then lost phase cannons to a hit. The forward shield collapsed and the Enterprise suffered hull breaches on B and C decks. With the forward shields down, the Xindi ships targeted the bridge and blasted the top off of it, killing the Enterprise bridge crew.
As boarding parties beamed aboard the Enterprise, T'Pol ordered Phlox to meet her and Archer in Engineering to complete his treatment since destroying the interspatial parasites would alter the timeline. In Engineering, Phlox discovered that the chamber used in the treatment had been destroyed by debris and was unusable. Archer remembered Phlox telling him that the parasites could also be destroyed by a subspace implosion which would destroy the Enterprise as well, but they don't have another choice.
Archer ordered T'Pol and Phlox to flee in a shuttlepod while he overloaded three plasma injectors to create the implosion since the Xindi were only looking for Humans, but both refused. Discovering that one of the injectors had been damaged, Archer sent Phlox to get a replacement from a supply locker which he used to successfully replace the damaged injector. Overcoming nearby security teams, Xindi boarding parties entered Engineering and killed Phlox. T'Pol started setting up the implosion as Archer laid down covering fire but was killed before she could finish. Archer took over, setting the controls on the warp core as he exchanged fire with the Xindi, taking several hits. With the last of his strength, Archer managed to trigger the subspace implosion moments before dying. The subspace implosion consumed the Enterprise, destroying the ship, its crew, the boarding parties, and the parasites. (ENT: "Twilight")
As hoped, the subspace implosion destroyed the interspatial parasites in both 2165 and 2153, resulting in Archer only suffering a concussion and no amnesia. Without the amnesia, Archer was able to remain in command of Enterprise NX-01. (ENT: "Twilight", "Zero Hour")