In the original timeline the five year mission was full of action. If we assume all TOS episodes take place in the 5-year mission and that they span over the full five years, I guess every 2 weeks the crew of the Enterprise and mainly Kirk had to deal with red shirt death, tricking god-like entities or computers, ripping of his shirt and fighting bare-handed against alien creatures, saving one planet and culture after the other.

This takes not into account the possibility that there where even other interesting events and adventures that are not shown on screen.

In the new timeline we see in Star Trek Beyond that the Enterprise has finished 3 years of its mission. We see Kirk on a diplomatic mission that fails and by his reaction we can guess that this is not the first mission of this kind and with this outcome. From his log entry we learn that he seems to be bored and disappointed and one he does not now when one day ends and the next starts.

So what about all the planets, entities and events that lead to the Enterpise adventures of the prime timeline? Where all the challenges still not discovered yet? Are the solved by antoher ship? Are they non existent in the new timeline?

closed as too broad by DaaaahWhoosh, Edlothiad, Dave Johnson, Ward, FuzzyBoots Jun 6 '17 at 18:01

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    Replaced by special effects explosions and senseless action scenes. – JRE Jun 6 '17 at 14:59
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    I don't think it's going to be possible to answer what happened to every single threat the Enterprise faced in its five-year mission. Both because a lot of the information probably doesn't exist, and because any answer that covers everything would be too long. – DaaaahWhoosh Jun 6 '17 at 15:01
  • It's not important to the core of the question, but TOS doesn't span over the full 5 years. TOS spans the first 3 and TAS spans the last 2. – ApproachingDarknessFish Jun 6 '17 at 15:08
  • Different timelines, different histories. – Ham Sandwich Jun 6 '17 at 20:00

They were handled by other ships.

In Star Trek: Into Darkness, Khan (posing as "Harrison") explains that as a result of Vulcan's destruction, the Federation aggressively explored outwards to the point where they found his derelict ship, the SS Botany Bay:

Harrison: But as a result of the destruction of Vulcan, your Starfleet began to aggressively search distant quadrants of space. My ship was found adrift. I alone was revived.

In the prime timeline, the Botany Bay was found by Kirk's Enterprise in the year 2267. Into Darkness is set in 2259/2260, so if we assume Khan was found a year or two earlier (sufficient time to construct the USS Vengeance), Starfleet in the Abrams timeline is approximately 10 years ahead of its Prime timeline counterpart in its exploration of the galaxy. The "frontier" that Kirk Prime made his career in has already been explored.

Khan is by no means trustworthy (he is operating under a fake identity at this point after all), but the fact remains that he did run into Starfleet many years early, so it seems reasonable to take him at his word on this matter.

Out of universe, this is clearly a throwaway line to justify sloppy chronology so they can cram names that people will recognizeKhan into the film. But I think it's the best explanation we can hope for.

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    So I think the answer to my follow up question "What happened to the Krall threat in the prime timeline?" would be "It was handled much later (between TOS and TNG) because of slower expansion and possibly by another ship and crew". Wow. So Kirk & Co. is not so special, given that all this crisis could be handled as easily by other crews and ships. At least all that would have had strong consequences if failed. – Hothie Jun 12 '17 at 9:12
  • @Hothie My thoughts exactly. – ApproachingDarknessFish Jun 12 '17 at 17:40

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