Spock, in command of the Enterprise, leads the bridge crew in trying to understand what happened. They have determined that the Narada is heading for Earth. Based on their red matter black hole technology, Spock reasons that the Narada must have traveled back in time from the future. He asserts that the Enterprise must regroup with the fleet, but Kirk says that in order to stop Nero they must go after him first.
Kirk believes that any delayed action will result in Earth being destroyed. An argument ensues which ends in Spock ordering Kirk's removal from the bridge, but Kirk fights off his security escort. Spock ends it by delivering the Vulcan nerve pinch to Kirk and ordering him placed in an escape pod.
The pod is launched and Kirk awakens to find himself on a snow-covered world known as Delta Vega, another planet in Vulcan's system. Picking up his gear, Kirk heads for the Starfleet station 14 kilometers away. He is chased down by a polarilla, which in turn is attacked by an even larger insectoid animal.
It chases Kirk into a cave, and when it finally attaches a tendril to catch him, it is spooked off by an elderly man wielding a lit torch. The man reveals himself to be Spock (Leonard Nimoy), Kirk's old friend, but the latter is skeptical.
Spock mind-melds with Kirk to make Kirk understand why he is there. He explains that 129 years in the future, in the year 2387, the impending supernova of the star Hobus threatened to destroy the home worlds of the Romulan Star Empire and throw off the political balance of the galaxy. Spock developed a stockpile of red matter, a substance that can be ignited to form a singularity -- a black hole capable of absorbing the matter of a supernova.
However, while he was en route, the star exploded much earlier than he'd predicted and Romulus was destroyed. Spock launched the red matter from his ship, the Jellyfish, to prevent further destruction to the galaxy. Immediately, Spock was confronted by a surviving Romulan mining vessel, the Narada, captained by Nero.
Spock tried to escape, but fed by the mass of the supernova, the resultant black hole captured both the Jellyfish and the Narada, creating a disturbance in the space-time continuum which sent both ships into the past. The Narada exited over 150 years in the past, where it confronted the Kelvin. Spock's ship entered moments later, but what appeared moments to him was 25 years for the Narada.
Nero captured Spock's ship when it finally appeared but kept Spock alive, marooning him on Delta Vega, so that he could witness the destruction of his own home planet, Vulcan. Just as Nero had to witness the destruction of Romulus.
Kirk explains he was left on the planet by the Spock he knows, who is in command of the Enterprise. The elder Spock is surprised, knowing that Kirk should be in command of the ship. It is then that Spock realizes that when Nero exited the wormhole and confronted the Kelvin, he altered history and created an alternate reality. Kirk asks Spock whether his father survived in the original timeline. Spock confirms that George Kirk saw his son take command of the Enterprise.
Spock leads Kirk to the Starfleet base where they meet this timeline's Montgomery Scott (Simon Pegg). Scott is an engineering genius who was also exiled to Delta Vega along with his alien assistant, Keenser (Deep Roy), after beaming Admiral Archer's beagle to an unknown location during a transporter experiment.
Spock informs Kirk that he must relieve the Vulcan's younger self of command by provoking him. He must show everyone that Spock is too personally and emotionally compromised as a result of Vulcan's destruction and the loss of his mother to lead the mission and command the ship.
Giving Scotty the mathematical formula for transwarp beaming, an operation originally devised by the older Scott, Spock sends Kirk and Scotty to the Enterprise. After rescuing Scotty from the Enterprise's coolant system, the two are spotted and almost immediately captured by security personnel, led by the guy who got into a bar fight with Kirk three years previously.
They are taken to the bridge where an astounded Spock demands to know how the two were able to transport on board the ship while it was in warp. Kirk refuses to answer and recommends that Scotty do the same. He asks why Spock doesn't feel any anger or have any emotion over the destruction of his planet and the death of his mother, who was murdered.
Kirk keeps pushing and provoking Spock until he finally snaps and starts beating Kirk, strangling him to the point of nearly killing him, before he is stopped by Sarek. Realizing how far he has gone, Spock relieves himself of duty and leaves the bridge. Kirk assumes command.
Following his outburst, Spock returns to the transporter room, where Sarek talks to him. Spock feels a rage he cannot control over the death of his mother. Sarek says that his mother would have said not to bother controlling it, and admits that he married Amanda because he loved her.
Meanwhile, on the bridge, Chekov devises a plan to get the Enterprise close to the Narada without the Romulans detecting them. They can follow the Narada and stop at Saturn's system, remaining undetected in the shelter of its magnetic field. Spock returns and endorses the logic of Chekov's plan. He offers to beam over to the Narada to get the black hole device and save Earth, the only home he has left. Kirk says he will go as well, to rescue Pike.
The Romulan ship deploys its drilling rig directly over San Francisco and begins to drill its hole near the Golden Gate Bridge. Warping into Titan's atmosphere, the Enterprise indeed remains undetected, and Kirk and Spock beam over to the Romulan ship. Scotty thought he would be beaming them to a remote and empty part of the ship, but it turns out to be an occupied portion.
After a brief firefight, Spock uncovers the location of the black hole device and Captain Pike by melding with an unconscious Romulan. When they board the Jellyfish, it recognizes Spock as its captain. The Vulcan finally figures out what's going on when the ship's computer confirms its stardate origin as 2387.
As Spock aboard the Jellyfish blasts his way out of the Narada, Kirk runs into more trouble when he finds the Romulans' bridge, where Nero and Ayel are waiting. Spock destroys the drilling rig before it can reach Earth's core, then goes to warp, and Nero orders pursuit. Kirk manages to gain control of Ayel's disruptor during a brief fight and kills him. He heads off to rescue Pike.
The ships drop out of warp and the Jellyfish turns to intercept and collide with the Narada. Nero orders all weapons to be fired, even though the ship still has red matter aboard; with his plan for revenge ruined, now he only wants to kill Spock.
The Enterprise arrives on the scene and destroys the missiles, allowing Spock to carry through with his plan to collide with the Narada. Inside the Narada, Kirk finds Pike, alive but injured due to his earlier torture. Scotty beams Kirk, Pike and Spock from their different locations right before the Jellyfish collides with the interior hull of the Narada and explodes.
The explosion of the Jellyfish ignites the entire stockpile of red matter on board, creating another black hole. Kirk offers to rescue the Narada but Nero refuses, saying he'd rather watch Romulus die a thousand times than accept his help. Kirk orders the Enterprise to open fire, blowing the ship apart with phasers and photon torpedoes.
The Narada is finally destroyed, but the gravitational pull of the black hole begins tugging on the Enterprise, keeping it from escaping, even with its engines running at warp speed. In a last-ditch effort, Scotty ejects the warp core and detonates it near the black hole. The resulting explosion pushes the Enterprise to safety, and the black hole implodes.
Spock Prime meets with his younger self to tell him that he helped Kirk directly so the two would form a friendship. As he leaves to help the remaining Vulcans establish a colony, Spock Prime raises his hand in the familiar live-long-and-prosper gesture. But notes that the unusual circumstances do not lend themselves to the famous greeting of the original series, so he simply wishes his younger self "Good luck."
Kirk is commended and given command of the Enterprise. He relieves Pike, who has been promoted to Admiral and is now in a wheelchair. Spock returns to the Enterprise and asks Kirk if he can serve as his first officer, to which Captain Kirk agrees and the Enterprise warps away.
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