In an alternate timeline, the Doomsday War was the name given to the seemingly endless series of battles that followed the appearence of the Doomsday Weapons in 2254.
Beginnings
In 2254 the USS Enterprise under the command of Captain Christopher Pike tracked a strong temporal signal. Arriving at the source, they discovered a Planet Killer and Klingon D7 class battlecruiser doing battle. The weapon easily destroyed both ships and began pulverizing whole worlds to duplicate and eventually produce an army of machines.
Starfleet Command immediatly withdrew all standing orders regarding exploratory missions, code named Operation: Ragnarok in an effort to stop the weapons.
By 2264 many worlds including Vulcan had been destroyed. In an act mutual self preservation, the Federation and Klingon Empire signed the HoH'egh accord, uniting the two powers for the first time in over a century. Commander Kargh was assigned to the Farragut, making him the first Klingon assigned to a Federation vessel.
First Major Breakthrough
In 2267 what was seen by some as a violation of the “non-exploration” directive, Captain James Kirk diverted the Farragut to investigate a time/space distortion phenomenon, later discovered to be a time portal, an artifact of an ancient civilization. This startling discovery resulted in the planet being named Gateway and the formation of Project Timepiece, a temporal research facility headed by Dr. Ann MacGregor.
Later returning from the planet, Farragut discovered the USS Constellation after it had been fatally damaged by a Doomsday Machine. In an effort to stop the Machine, Constellation commander Commodore Matthew Decker stole Shuttlecraft Jefferies from the Farragut and piloted it on a suicide mission into the device. Decker was unsuccessful, having seemingly exploded inside the Machine, but data from his attempt were used to conduct a second effort, using the more powerful reactors from the derelict Constellation. Their success at this attempt was heralded as the first breakthrough in the Doomsday War.
Correcting the Timeline
It wasn't until 2268 that Ann MacGregor and Spock (protected from the changes) on Gateway discovered the alterations that had caused this devastating conflict. Farragut was immediatly summoned to the planet where they learned of the recent fluctuations in the natural flow of time due to the premature destruction of the USS Enterprise in 2254.
In an attempt to correct the polluted timeline, Farragut travelled back in time to 2266 and joined the USS Daedalus and USS Enterprise-A (also from the future) in defeating the Doomsday Machine by sending it into the 24th century where it would be quickly dealt with by Starfleet. The Farragut returned to its correct time. Once the timeline was restored, the ship changed back into the Enterprise and the events of the war ceased to exist. (STNV: "In Harm's Way")
External Links
Star Trek: New Voyages website
Timeline of events in the Doomsday War