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After Kirk was thrown out of the USS Enterprise and he met Spock Prime, Spock Prime suggested to Kirk that he should take over from Spock and become the captain of the USS Enterprise.

Well, in the original timeline, Kirk was an awesome captain, but this wasn't the original timeline. Lots of things were different. For example, in the original timeline, Kirk's father didn't get killed just after his birth. This small change can have a profound effect on one's personality. He was raised by his father. His father became his early motivation to him (mentioned in Star Trek (2009) I believe). In the new timeline, he got his motivation to join Starfleet from Christopher Pike. Up until that point, he was a complete jerk who would pick bar fights over a girl's name.

In-universe, whatever happened might have given Kirk the same or similar personality by luck, but what made a genius like Spock Prime think that Kirk would be a better captain of the USS Enterprise than young Spock? Spock was appointed captain by Starfleet and Kirk was just thrown out of the ship over a barbaric issue.

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    "Know thyself". Spock to the point of the destruction of Vulcan had the same upbringing in both timelines. He knew inside he wasn't a captain. – Jane S Nov 9 '15 at 10:20
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    I'm pretty sure that original timeline Kirk picked barfights over alien girl's names too! – JamesRyan Nov 9 '15 at 18:55
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There are a couple of reasons why Spock Prime would have told Kirk to take command:

Spock Prime didn't know of Jim Kirk's altered past

Spock Prime was genuinely surprised to see Kirk was not the captain. Given he had only recently been marooned on the moon, he likely had zero chance to actually find out that the history of this Kirk was different to Kirk Prime.

Also, Spock Prime had spent decades with Kirk Prime. He knew the type of person he was. Tenacious, determined and resourceful. The fact that Kirk had managed to get to his cave in the first place was as good an indication as any that he was in the same mould as the Kirk he knew.

Spock knew he wasn't a good captain

Nosce te ipsum. Know thyself. Up to when Vulcan was destroyed, the timeline for both Spocks was identical very similar insofar as both his parents were still alive and he spurned the Vulcan Science Acadamy to join Starfleet. But given my previous point above where Spock Prime had no real idea as to the history, he knew in himself that he wasn't really captain material. A fine officer, but not the person with the intuitive, illogical leaps that makes a good captain. He also knew that an attribute of a captain like Kirk is his ability to break the rules when it suited him. The younger Spock was yet to learn this lesson (from Kirk!).

A classic example of how well Spock Prime understands himself, he knew that younger Spock was severely emotionally compromised (as he was himself) and that it would take little to get him to break.

Put these together would be a reasonably good starting point for Spock Prime to assume that Kirk would be a better captain than he himself would be, so it's... logical for him to tell Kirk to regain the captaincy of the Enterprise.

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    But was the timeline for the two Spocks identical until the destruction of Vulcan? According to memory alpha, Spock prime was science officer (not first officer) under Pike in 2254, one year before the alternate Enterprise is even constructed in Iowa ("She's brand-new") – Hagen von Eitzen Nov 9 '15 at 17:44
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    Indeed, at a minimum, Spock's career path was altered by the delay and redesign of the Constitution Class. Changes to The Federation as a result of the Kelvin attack, both political and technological, may have altered even Spock's early life further. – Politank-Z Nov 9 '15 at 18:36
  • @HagenvonEitzen Good pick up, I missed that :) I would say that his formative years on Vulcan, where the Vulcan Science Acadamy seemed to follow very traditional schooling, would have been mostly unchanged. Of course there may be some variances, but there were none as far as life-changing events such as being orphaned. – Jane S Nov 9 '15 at 21:01
  • Still, though, Spock Prime had served as Captain of the Enterprise for at least a few years. He always had a difficulty relating to humans, and it's quite possible that he knew even an inexperienced Kirk would make a better captain under the circumstances due to his natural ability & charisma. – Omegacron Nov 9 '15 at 22:25
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    @Omegacron Also remember that young Spock had not yet learned his "humanity" from Kirk, so his alternate self would probably end up suffering "death by regulations" :) – Jane S Nov 9 '15 at 22:32
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A lot of the answer is "Because that's what the writers wanted to happen". They wanted Kirk to be in charge. In the eyes of the writers, Kirk's lack of experience is meaningless compared to his huge personality.

Also a strong element, young Spock is pretty heavily swung to his logical Vulcan side, while adult Spock is far closer to his human side, and is portrayed as more mature and more comfortable in his skin, and we the viewer are supposed to feel that is the "better" Spock. So mature Spock thinks that young Spock does not have the right temperament to lead this mission while brash bold Kirk does.

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Spock's motivation after he travels back in time is to prevent Nero from significantly altering the timeline.

This is covered in the prequel comic Star Trek: Countdown.

Long story short, there is a disaster and Spock is able to save Vulcan, but not Romulus. Nero sees this and blames Spock for saving his own planet while letting Romulus be destroyed, so he goes nuts, gets a bunch of tattoos, and outfits his mining ship with Borg technology.

There is a bit of a space fight, ending with Nero and Spock being sucked into a black hole. In the prime universe, this looks like Nero and Spock both die. But then they pop out in the Abrams-verse (Spock pops out 20 years later, because that's how black hole time travel works).

So when Spock pops out, one of his main goals is to prevent Nero from modifying the timeline. However, he's too late, since Nero has a 20-year head start on him.

That's why when Spock sees that Kirk isn't the captain, he tries to remedy that: that's a very personal and very obvious modification of the timeline, so Spock does his best to right the wrong and get things back on track. This is also why Spock helps them track down Scotty and come up with the equations that Scotty should have developed.

The events of the comic are condensed into the mind-meld flashback in the movie, which loses a lot of the backstory and motivations.

The core point is this: Prime Spock's primary motivator in the Abrams-verse is to prevent Nero from manipulating the timeline. Making sure the Enterprise crew is "right" is part of that goal.

  • I have read Star Trek: Countdown... Your story is plain simple wrong. – Lobo Nov 9 '15 at 18:02
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    @SS-3.1415926535897932384626433 Can you be more specific? I'm admittedly paraphrasing, but the central point is that Spock's motivation in the Abrams-universe is to prevent Nero from modifying the timeline. Making sure the Enterprise crew is "right" is part of that goal. – Kevin Workman Nov 9 '15 at 19:05
  • Spock didn't go inside the black hole by choice. – Lobo Nov 9 '15 at 19:08
  • Also, Romulus never voted against the Red Matter. They were just ignoring Spock's calculations, but later they accepted it. – Lobo Nov 9 '15 at 19:10
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    @SS-3.1415926535897932384626433 I've edited my answer. – Kevin Workman Nov 9 '15 at 19:23
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Because, Spock Prime knew that was the only way, not only to save the Enterprise, but so that they would become friends. Otherwise, the resentment for each other, instead of being released, would just grow.

Update: They continued to fight by each other's side in "Into Darkness". If Kirk hadn't taken back the ship they probably logic wouldn't be friends.

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    Welcome to the site! :) I wonder, do you have any evidence for your ideas here, or anything to add to this answer to flesh it out. As you spend a bit more time here and come to read other answers you'll see that we usually like answers to come with a why - that's what will get you reputation points and as you accumulate them, you'll be able to leave short comments like these in the comments section, their real home :) – Au101 Nov 9 '15 at 17:30

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