The Kelvin timeline or alternate reality was a parallel universe created in 2233 with the temporal incursion of the Narada, a Romulan civilian mining vessel under the command of Nero from the year 2387. The alternate reality differed from the primary universe in a number of capacities, including the attack upon the USS Kelvin, the launch of the USS Enterprise in 2258, and the destruction of the planet Vulcan by the Narada.
In the primary universe, a supernova in 2387 threatened the entire galaxy. Ambassador Spock was able to halt the supernova, via the use of red matter to create an artificial singularity, or black hole, which absorbed the exploding star, but was too late to save the planet Romulus from destruction. The Narada, a Romulan mining ship under the command of Captain Nero, was pulled into the black hole, followed by Spock's ship, the Jellyfish.
The Narada was pulled into a black hole and appeared in the year 2233. Nero launched an attack on the Federation starship USS Kelvin. The Narada severely damage the Kelvin with its powerful weapons but was crippled when George Kirk rammed his ship into it. The disabled Narada soon attracted the attention of the Klingons. A fleet led by Captain Kor of the IKS Klothos attacked. The Narada's crew did their best to repel the Klingons, but despite killing many could not hold back the stronger Klingon force.
Destruction of Vulcan
The Narada attacked Vulcan, destroying all of the Starfleet ships that attempted to intervene. Though the Enterprise crew tried to foil this plan, the Narada successfully drilled into the core of the planet and placed Red matter there, creating an artificial black hole at the core, which promptly consumed the planet.
Attack on Earth
The Narada then attempted to destroy Earth in a similar manner, but through the actions of Captain Kirk and Spock, an artificial black hole was created which then consumed the Narada.
After stopping at the Aldebaran colony, the Enterprise prepared to leave the Milky Way galaxy when it intercepted a record-marker from the SS Valiant. Spock was able to analyze the memory banks, revealing an unknown force in the region that forced her captain to destroy his own ship.
Continuing its course to our galaxy's boundary, the Enterprise encountered an unusual force field known as the galactic barrier. Nine crewmembers died, and another was injured—Kirk's friend, Lieutenant Mitchell. The Enterprise also lost her warp capability.
Under the care of Leonard McCoy, Mitchell began to exhibit unusual powers, such as levitation and telepathy. At a senior staff meeting in the briefing room, the crew agreed to maroon Lieutenant Mitchell on "another Delta Vega."
Arriving at Delta Vega I, Kirk and McCoy prepared Mitchell for exile when he attacked Kirk with a blast of energy from his hands. McCoy made a split decision to knock him out with a sedative. He was later beamed down to the planet, with Kirk and Spock, while Scott and Kelso searched the facility for materials they needed to restore the ship's warp drive.
Mitchell revived, escaped his force field, then stunned Kirk and Spock with the energy from his hands. He later met Kelso, and forced his former friend to shoot and kill himself with his phaser.
Scott revived Kirk and Spock, telling them Mitchell had escaped and Kelso was dead. Kirk made a command decision to confront Mitchell, ordering Spock to quarantine the planet and leave if he had not returned in three hours.
Awaiting him in the desert, Mitchell demonstrated his power of illusion to Kirk by transforming the landscape around them into the bar from Iowa. Returning the landscape to its original state, Mitchell forced Kirk to kneel before him and beg forgiveness for his failure and his humanity. As he did so, Spock came up behind Mitchell and nerve-pinched him. Kirk ordered Spock to stand back, then shot and killed his friend.
Kelso and Mitchell were buried in space. Spock later joined Kirk in the briefing room, offering to play chess with him. Kirk accepted the offer, and Spock left for engineering, leaving him alone in the briefing room.
A fearful Federation
By the late 2250s, the head of Starfleet, Admiral Alexander Marcus, had become increasingly became concerned about tensions with the Klingons, who since they were first encountered had conquered and occupied at least two planets and had fired on Federation ships half a dozen times. Fearing that the Klingons were comming his way, Marcus went in search for potential resources. He found the SS Botany Bay, recovering its seventy-three occupants. He awoke Khan Noonien Singh from cryogenic stasis, and blackmailed him into designing ships and weapons to prepare for the coming war.
The Treaty of Organia was in existence by February 2259, but on the eve of the founding of Sherman's Planet, there was a dispute about it.
A year later, the Enterprise violated the Prime Directive, altering the civilization on Nibiru during a scientific mission on that planet.
Around the same time, Khan turned on Starfleet, coercing a member of Section 31 into bombing a base of theirs in London. During an emergency meeting in San Francisco, Khan attacked before escaping to an uninhabited area of Qo'noS using the confiscated transwarp beaming formula. During the attack, Admiral Pike was killed, and a vengeful Kirk was given permission to find and terminate Khan. The Enterprise was outfitted with seventy-two advanced long-range torpedoes, with the intent of using these to execute him from orbit.
When the Enterprise arrived at Qo'noS Kirk opted to apprehend Khan, rather than firing a torpedo on his location. When they found him, Khan killed the Klingon patrol that had intercepted Kirk's away team and submitted to his authority. Aboard the Enterprise, Khan explained his involvement with Marcus, after McCoy and Carol Marcus discovered his crew were contained inside the missiles supplied by the admiral.
Marcus soon arrived on the USS Vengeance, and opted to destroy the Enterprise to cover up the conspiracy. Fortunately, Scott had stowed away on the Vengeance and deactivated its weaponry, giving Kirk and Khan time to space-dive and commandeer the ship. Khan then betrayed Kirk, killing Admiral Marcus, and threatened to resume bombarding the Enterprise unless his people were beamed aboard. The missiles were beamed aboard, but Khan reneged on the deal, forcing Spock to detonate the missiles; however, McCoy had removed the cryo chambers from the missiles before they could be used against the Vengeance.
Both ships were crippled and began descending due to Earth's gravitational pull. Kirk reactivated the Enterprise's warp core before it crashed, but at the cost of fatally poisoning him. When the Vengeance crashed in San Francisco, Spock beamed down to execute Khan in retribution, but McCoy realized Khan's blood could be used to revive Kirk, so Uhura beamed over to stun Khan repeatedly so that Spock could simply knock him out. McCoy then performed a blood transfusion, saving Kirk's life. Khan was placed back in stasis with the rest of his people.
Almost a year later, Captain Kirk presided over a memorial for the lives lost because of Khan and Marcus. The refitted Enterprise was rechristened and sent on a five-year mission with the aim of promoting a less militaristic direction for Starfleet.
Following negotiations between the Teenaxi Delegation and the Fabona Republic, the Enterprise docked at Yorktown Station to resupply. During this time, Ambassador Spock has died, Spock and Uhura take a time out from their relationship and Kirk applies for promotion to Vice Admiral.
An escape pod is found and its occupant, Kalara informs her that her ship has been stranded on Altamid. Commodore Paris agrees to let Kirk and the Enterprise enter the Necro Cloud to assist her. However, once in orbit around Altamid, the Enterprise comes under attack by a swarm of ships. The Enterprise tried to escape but was crippled and boarded by Swarm drones led by warlord Krall and Manas. Kirk and his crew were then forced to abandon ship before it's saucer section crash landed on Altamid. However, most of the crew had been captured save for Kirk, Chekov, Spock, Kalara, McCoy and Scotty.
Krall's revenge on the Federation
In 2263, Krall, formerly Captain Balthazar M. Edison and commanding officer of the USS Franklin, discovered – from Starfleet logs, accessed through a captured Magellan probe – that this weapon was the second piece of the Abronath had been placed into storage on the USS Enterprise. He dispatched Jessica Wolff, now "Kalara", to lure the Enterprise to him.
Upon the arrival of the Enterprise at Altamid, Krall attacked with his Swarm. He destroyed the Enterprise, captured most of the crew, and eventually coerced Ensign Syl into relinquishing the second Abronath piece. His weapon complete, Krall departed Altamid with his Swarm to wipe out all life from the nearby Starbase Yorktown, whose multicultural population he saw as the epitome of the Federation's degeneracy.
Krall's Swarm overwhelmed Yorktown's defenses and were on the verge of breaking inside when he was engaged by the USS Franklin, commanded by Captain James T. Kirk. The Franklin used a VHF radio broadcast to disrupt the Swarm's internal communications network and destroyed most of them. Krall managed to enter Yorktown, but the Franklin physically stopped his ship short of his destination.
Having drained many Enterprise crew members before and after the battle, Krall had regained much of his Human physiology and was thus able to disguise himself as a Starfleet officer. This allowed him to make his way unimpeded to the central atmospheric processor on Yorktown, where the Abronath's effects would be disseminated throughout the station. He was intercepted by Kirk, and the two fought while Montgomery Scott redirected the processor to vent into space; Kirk then ejected both Krall and the Abronath out of Yorktown. Shortly after, Krall was consumed by the Abronath, leaving only the Starfleet insignia from his stolen uniform.
During Enterprise-A's construction, Captain Kirk and Dr. McCoy were then assigned to the USS Endeavour. Commander Sulu was assigned to the USS Concord and Commander Scott then took a position at Starfleet Academy. Commander Spock and Lieutenant Uhura then took a sabbatical to New Vulcan to assist in rebuilding the Vulcan Science Academy.
Following the defeat of Krall, a new Enterprise was completed at Starbase Yorktown and assigned to the surviving Enterprise crew to continue their five-year mission.