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While I think the Star Trek (2009) movie was pretty cool looking, its story-line wreaks total havoc with all the existing post original series content.

I know that Gene Roddenberry was very strict about what was considered canon in the past, basically anything he didn't like well (like the animated series). But now, since his death, it seems like all the later series are considered canon.

Is the latest Star Trek (2009) considered canon?

Since the events of the 2009 movie take place in an alternate timeline to that of the original series, there is no logical problem with it being canon.

The hows and whys are detailed here: Bob Orci Explains How The New Star Trek Movie Fits With Trek Canon (and Real Science)

Being an "official" product, and given the fact that Gene has passed -- Yeah, I would consider it canon.

Like it or hate it (I enjoyed it myself) it does conveniently "reboot" the timeline in a manner that lets it remain canon without making any of the previous films inaccurate to the new storyline.

It's probably best to think of it as "new" canon. They rewrote history so continuity with the old series doesn't matter. Which lets them play with those tensions, of course--those of us who know the old material can enjoy the changes to the universe, a sort of meta-level of writing for the "in crowd".

The Uhuru/Spock love story could be canon if you take into consideration the timeline was altered as soon as George Kirks ship encountered the anomaly at the beginning of the movie, from that point in time an alteration to the timeline has occurred. Whatever the consequences of that were, they occurred in such a way that it facilitated sometime in the future a relationship between Uhuru and Spock that would not have occurred otherwise.

It has its own canon. It's not the same as Gene Roddenberry's canon. I was surprised at seeing Spock's love story with Uhura in the reboot because they're not the way I know the characters. Uhura appears to be attracted to Spock in 'The Man Trap' (Who isn't) and tries to flirt with him and he has no idea what she's doing and she gives up really quickly while making a quip at Spock. She's attracted to him. There's no indication that she's in love with him. Spock doesn't appear to be any close to Uhura than he is to Sulu or Chekov or Scotty. Uhura even says that Kirk is the "closest thing [Spock] has to a friend." When Spock dies in Wrath of Khan it's Kirk who is at the glass. Uhura isn't mourning more than anybody else. Kirk is the one who risks everything in Search for Spock to bring him back. In other words, they are not together in TOS canon after 79 episodes and 6 movies and even in the reboot Spock Prime (Who is from the TOS timeline). Now, the writers may have thought about having Spock and Uhura pursue a romance and it may have been because of racism as they didn't, but the point is that they scrapped the idea and they weren't even shown to be that close. There have always been fans who think Spock would work well with Uhura but it wasn't an official relationship in TOS and Spock was actually a lot closer and more affectionate toward Captain Kirk. People may tease K/S "slasher" and say that this isn't canon either but the characters are still a lot closer.

I was surprised by the pairing in the reboot because it was against the relationship that had been (Or hadn't been) established for over 40 years. But then people always point out that it's an alternative reality/timeline. In THAT canon, Spock has a pre-existing affectionate relationship with Uhura before he befriends Kirk. At the time of the first movie Uhura appears to be his only friend, she is a respected student and apparently (Although not really stated clearly) a lover. Part of the reason I felt a bit let down by the romance (Despite good acting and good chemistry) was because they had taken a very interesting character like Spock and made him almost into a typical archetypal male hero. Cool thing about Spock was that he could be a strong male character without constantly chasing chicks the way Kirk did. Also, Uhura is the only frequent female character. It doesn't seem particularly creative to match Spock with the only female around and also have Kirk chasing her to create a love-triangle. In TOS Uhura was a respected member of the crew and she wasn't automatically turned into a love interest for all the males around her. Now one of Uhura's main plotlines is that she's pining over Spock. Despite my disappointment, it IS a different timeline and people will point that out. But then they'll go ahead and claim that Abrams making Spock-Uhura a canonical relationship in the reboot makes it canonical in the alternative timeline. IT DOESN'T. If it's a different canon, then it's a different canon. End of story. The canon overlaps when Spock Prime comes into the reboot universe but the character's stories are different. What happens in the reboot timeline only happens in the reality of the reboot. If we're so obsessed with canon to the point of making fun of "slash fangirl" then we shouldn't be claiming that an alternative timeline effects the canon of the original timeline. By that logic, Spock's mother is dead at the beginning of TOS, which we clearly see that he isn't, and Vulcan has been destroyed which it clearly hasn't and Kirk has not brother called Sam which he clearly does.

After my little rant, the reboot has A canon but it isn't the same as Gene Roddenberry's canon. Pine's Kirk is BASED on Shatner's Kirk but he's the alternative timeline Kirk. He's not exactly the same guy as TOS Kirk.