Star Trek: The Alternate Reality Saga

The Federation starship USS Kelvin investigates a "lightning storm" in space. It turns out to be a black hole and the Narada, a Romulan mining vessel, emerges from it, attacking the Kelvin and capturing its captain, Richard Robau. The "Narada" crew takes Captain Robau to the bridge and interrogates him about the whereabouts of Spock, after which the Romulan captain, Nero, kills him. Learning of Robau's death, first officer George Kirk takes command and sacrifices himself and the Kelvin by colliding it into the Romulan ship in order to allow the rest of the crew to escape. During the escape, George's wife Winona gives birth to a son: James Tiberius Kirk. Without the influence of his father, James Kirk grows up as a rebellious youth.

On Vulcan, a young Spock—half-Vulcan, half-Human—is tormented by bullies for the 35th time and reacts emotionally for the first time by lashing out at one of his bullies. His father, Sarek, tells him that he has to choose his own path and his own destiny. Many years later, Spock stands before the members of the Vulcan Science Academy, having applied there and the Starfleet Academy. They offer him a place in the Vulcan Academy, noting his outstanding record, despite his "disability" (which the Vulcan Science Council states) of being half human. However, he declines the position at the Academy and instead joins Starfleet Academy, ultimately graduating and becoming a teacher.

At age 25, Kirk has grown into an intelligent but reckless and cynical young man. He meets Uhura and Captain Christopher Pike in a bar in Iowa, where Pike convinces Kirk to enlist in Starfleet Academy and follow in his father's footsteps. During his eventful three-year education on Earth, he is suspended for cheating on the Kobayashi Maru test designed by Spock. Despite this, Kirk is smuggled on board the USS Enterprise by his friend Dr. Leonard "Bones" McCoy, as it and six other ships, hastily manned by combination of Starfleet and cadet crews, is sent on its first mission to investigate a distress signal originating from the planet Vulcan. Captain Pike commands the ship with Spock as his first officer; Uhura is also assigned to the ship. En-route, Kirk realizes that the situation is very similar to the one that occurred 25 years ago on the day of his birth, and with the help of McCoy and Uhura (who recently intercepted a transmission detailing a Klingon confrontation with Nero's ship), they manage to convince Pike and Spock that the Enterprise is headed into a trap. The Enterprise exits warp, arriving at a debris field of Starfleet ships destroyed by Nero's ship the Narada, which is using a drilling apparatus to tunnel to Vulcan's core. Pike surrenders to Nero after promoting Spock to captain and Kirk to first officer in order to give Kirk and Hikaru Sulu a chance to destroy the drill. Nevertheless, Vulcan is destroyed when Nero uses a small amount of "red matter" to create an artificial black hole within the planet's core. Six billion Vulcans die, along with Spock's human mother, Amanda. Spock estimates that only around ten thousand of his people remain, quoting that the Vulcans are now an "endangered species." When Uhura follows him to comfort him, he shows emotion for the first time, it also becoming clear Uhura has feelings for him that Spock seems to reciprocate.

Nero proceeds on a course for Earth with the same intentions. Kirk wants to pursue Nero immediately but Spock insists that the Enterprise should regroup with the fleet as per their orders. Spock has Kirk forcibly removed from the Enterprise and stranded on the nearby ice planet Delta Vega. He is rescued by an aging Vulcan, revealed to be Ambassador Spock from the future. This elderly Spock explains that 129 years into the future, he will have tried to save Romulus from being destroyed by a nearby supernova, using the red matter in his ship to create a black hole that would neutralize the threat. Spock manages to stop the supernova, but not in time to save Romulus, resulting in Nero's vow to exact revenge on Spock and the Federation. The resulting black hole transports Spock's ship and the Narada into the past, which also creates an alternate timeline from the original series. Spock takes Kirk to a nearby Starfleet outpost where they meet Montgomery Scott, a master engineer and pioneer of transporter technology. Using "transwarp transportation", a development that Scott will perfect in the future and which Spock has memorized the equations for, Scott and Kirk are transported back to the Enterprise and taking Ambassador Spock's advice, Kirk goads the younger Spock into attacking him. Spock is forced to relieve himself of command on the grounds that he is emotionally compromised by the current mission, leaving Kirk to become the acting captain of the Enterprise.

Captain Kirk takes the Enterprise to Earth, intending to stop the Narada on his own. Spock, Scotty, and Russian math-whiz Pavel Chekov bring the Enterprise to Titan (one of Saturn's moons) in order to take advantage of Saturn's magnetosphere to conceal themselves from Romulan detection, allowing Kirk and Spock to beam aboard the Narada and stage a surprise attack. While Spock steals Ambassador Spock's captured ship and lures the Narada away from Earth, Kirk rescues Pike. With the assistance of the Enterprise, Spock then collides Ambassador Spock's ship into the Narada, detonating all the red matter and creating a black hole that, aided by a full barrage of the Enterprise's weaponry, destroys the Narada. Kirk, Spock, and Pike are rescued just in time by the Enterprise via transporter. They offer Nero assistance, but he remains on his ship, choosing to die rather than accept their help. They manage to escape the event horizon thanks to Scotty's quick thinking.

Back on Earth, Pike is promoted to Admiral and Kirk is commended and promoted to captain and given permanent command of the Enterprise. Ambassador Spock visits his younger self and explains that he helped Kirk directly to ensure that the young Spock and Kirk would come to an understanding and become friends. The elder Spock accompanies the survivors to establish a new colony. The younger Spock, convinced to stay with Starfleet, requests to be posted to the Enterprise as first officer. As the Enterprise warps away, the elder Spock recites the series's tagline:

“ Space: the final frontier. These are the continuing voyages of the starship Enterprise. Her ongoing mission: to explore strange new worlds, to seek out new life-forms and new civilizations; to boldly go where no one has gone before. ”

The USS Enterprise is sent to the planet Nibiru to observe a pre-warp civilization. Captain James T. Kirk and Spock attempt to save the inhabitants from an imminent volcanic eruption which would wipe out the civilization. When Spock's life is jeopardized, Kirk breaks the Prime Directive, exposing the Enterprise to the planet's civilization during Spock's rescue. A number of indigenous people begin to worship the ship as it leaves. Called back to Earth, Kirk is demoted to First Officer and Admiral Christopher Pike re-assumes command of the Enterprise. In London, Starfleet agent John Harrison bombs a secret "Section 31" installation. In San Francisco, Pike and his first officer attend an emergency meeting of high ranking officers at Starfleet headquarters. The meeting is attacked by a gunship piloted by Harrison, who kills Pike. Kirk destroys the gunship, but Harrison flees.

With Pike dead, Admiral Alexander Marcus authorizes Kirk to hunt down Harrison, who has used transwarp beaming and fled to the Klingon homeworld of Kronos. Since Kronos lies deep in Klingon territory and the Federation is on the brink of war with the Klingon Empire, the Enterprise is supplied with 72 long-range prototype photon torpedoes, and is ordered to fire them at Harrison's location once he is found. Thinking that the torpedoes could be dangerous to the ship, Montgomery "Scotty" Scott refuses to take them aboard and tenders his resignation, whereupon Pavel Chekov is promoted to Chief Engineer. Admiral Marcus' daughter, scientist Carol Marcus, joins the crew under a false identity.

Arriving at the Klingon homeworld, the Enterprise's warp core malfunctions. With repairs underway, Kirk, Spock and Uhura use a previously commandeered trader ship to reach Kronos. After being detected by Klingon patrol ships, the three are forced to land. Despite Uhura's attempts to negotiate, the Klingons prepare to kill the trio. Harrison wipes out the Klingons and confronts the landing party, but surrenders after learning the precise number of photon torpedoes aimed at him.

Returning to the Enterprise, Harrison reveals his true identity: Khan Noonien Singh, a genetically engineered superhuman, who has been in cryo sleep for 300 years after his dictatorship and that of other super humans fell during Earth's Eugenics Wars. He advises Kirk to examine the 72 prototype torpedoes and also tells him a set of spatial coordinates. Kirk orders Leonard McCoy to examine the torpedoes, and contacts Scotty on Earth to check the coordinates. The torpedoes are found to each contain a genetically-engineered human in cryo sleep - the remaining members of Khan's colleagues. Khan explains that Admiral Marcus awakened him to use his superior intellect and savagery to develop advanced weapons for a war with the Klingons, keeping his colleagues as hostages. Kirk realizes that the Enterprise's warp core had been sabotaged on Admiral Marcus’ orders, making the covert operation to kill Khan a one-way ticket.

Scotty arrives at the coordinates and finds a secret Starfleet shipyard, which he infiltrates. The Enterprise's warp core is repaired, but the ship is soon confronted by an unregistered Federation battleship, the USS Vengeance - a massive vessel built for combat which dwarfs the Enterprise. Admiral Marcus reveals himself as the commander of the Vengeance, demanding Kirk hand over Khan. Kirk refuses, and the Enterprise warps toward Earth, to have Khan stand trial.

In Earth's orbit, the Enterprise is attacked by the Vengeance. With the Enterprise severely damaged, Kirk offers to hand over Khan and the 72 bodies in cryo sleep in exchange for the lives of his crew. Marcus refuses, beams his daughter to the Vengeance, and orders the destruction of the Enterprise—when the Vengeance suddenly suffers a complete power outage, caused by Scotty who had boarded the ship at the secret shipyard. As the Enterprise weapons are too damaged to continue the fight, and knowing that Khan was the designer of the Vengeance, Kirk allies himself with Khan and boards the ship. They reunite with Scotty and take the bridge. Meanwhile, Spock contacts Spock Prime to learn of Khan's history and how to defeat him. Khan betrays Kirk and takes control of the Vengeance, killing Admiral Marcus. Khan negotiates with Spock, beaming Kirk and his boarding party back to the Enterprise in exchange for the 72 cryo torpedoes.

Khan plans to destroy the Enterprise, but Spock reveals that real – and armed – torpedoes were beamed to the Vengeance, keeping the cryo pods on the Enterprise. The torpedoes incapacitate the Vengeance and anger Khan, who believes that his 72 colleagues have been killed. Both ships start descending towards Earth's surface. At the cost of his life, Kirk re-aligns the warp core, enabling the crew to regain control of the Enterprise. The Vengeance crashes into downtown San Francisco, but the crash does not kill Khan. Khan tries to escape in the chaos, but is pursued by Spock. McCoy discovers that Khan's blood may reanimate Kirk and Uhura prevents Spock from killing Khan, capturing him instead.

In the aftermath, Kirk is revived and returns to duty as Captain of the Enterprise. Khan is sealed into his cryo pod and stored away with the rest of his crew. As the film ends, a restored Enterprise is re-christened and departs for a 5-year mission of exploration.