This is a TL;DR type of post. If it is TL;DR for you, head to the end of the post for the short version of this hot mess of a post. You have been warned.
If we're into the third year of the five year mission, crazy thought. What if this timeline gets re-integrated into STOs timeline. And so history changes, but the deviations aren't as much as you'd believe. Like imagine if you will that the first two seasons of the TV show still happen more or less the same, except with the new ship. Now imagine if you will, that time continues on more or less the same minus these small differences. However, this movie (and subsequent movies after) replace the least liked seasons of TOS, Season 3 and TAS.
Oh, I'll get to why in a bit on that.
Also, if you pause the trailer at the 1:05 mark and you take a look at that armor, it closely resembles the Voth's armor. The Franklin might've found a civilization that is a spin-off (so not the right word, but I'm going with it) of the Voth, but who are super friendly and outgoing. They decide that because these Voth do technically have a right to be on Earth, they'll bomb the heck out of the place because "liar!". In fact, don't the Voth have an arm weapon? However, I'll get to that in a minute, because that arm isn't in the right century though, is it?
Now this still holds true that this is a new entity that the Federation would have to face. As although they are like the Voth, these guys would've broke off from them so they are all peaceful and were relatively nice before the Franklin bombing them badly, before the Voth (and Na'kuhl, and I'll explain that in a minute or two) manages to stop the Franklin and downing it. Hence why it is now scrap. Since the Franklin bombed them, this would probably make them a wee bit upset, right?
Now, there have been instances were you could see things that I could swear don't belong in the 23rd Century, like that swarm that looks similar to the Obelisk's drones. What if the Na'kuhl came back in time (either our Na'kuhl or the Kelvin's timeline, but what the hell, we'll say both for good measure) and handed these Voth an Obelisk (or just the drones) and also their 25th century gear.
Due to all the screwing around that happens due to the Na'kuhl, Narada and also us in STO, both the Kelvin and Prime timelines, are screwing things up so badly that the only way to fix things is for the somehow merging of the two timelines. Also, yes, most people will know that the timeline has changed, because you might as well go with it as it is the end of the world type of situation. Though I guess this is an end of the universe type situation.
The place that both timelines eventually merge? The Battle of Procoyn (spelling, dammit) V. While Enterprise (or them on the Franklin) probably doesn't get to see this fight, this would be explained by Captains from an alternate 23rd Century and the Alliance characters of the 25th century are fighting to save both timelines. They (Enterprise crew) do however need to survive their little conflict or this merging timeline thing doesn't happen. They also can't send a ton of people because technically we're all fighting to save the two timelines at the current moment. Also, yes that female who helps Kirk is probably a time traveler (from that era, but a Time Cop nevertheless) who gets to explain all of this lovely stuff.
This allows them to give a nod over to Star Trek Online as we're the Captains that are helping out in the Battle of Procoyn (yes, spelling I know) V, and also giving a rational reason as to why none of the Captains (TOS, ENT, TNG, etc.) can participate in the Battle, because then you'd need to define these characters from STO and you still want STO to keep running for quite some time still. When STO's life span is over, they can solidify these 4 Captains (FED, TOS, RRM, KDF). See? I can even tie in STO into this mess and make it legit, so I have to be correct!
Technically, things will become new due to the fact that the two timelines are now one fluid (not solid) timeline. This allows Paramount and CBS to rescript the past, but also keep things intact. It would allow them to rewrite history, but also go "hey, TNG still occurs as is" so that the old stuff still works with the new stuff (except maybe different looking ship designs). That might be why they were in a war with Axanar, is because this might be what's going on and not only are they protecting the IP, they didn't want someone using the old designs because they are technically no more. Design wise, not actually gone gone. Also, it allows them to cherry pick every story that has occurred with Star Trek characters, because it makes sense.
And yes, for them to explain why the timelines needed to be merge that would probably break everyone's brain, but hey, everyone can settle for a Doctor Who like explanation. That'll usually solve things. Also, both Vulcan and Romulus are gone in this new connected timeline I'm theorizing because we need those tragedies to still occur otherwise the whole things goes kablewy.
Yeah, crazy theory is crazy, and I totally just made this craziness all up in the last half hour to forty-five, but think about it this way.
TL;DR - I call time travel shenanigans, both Prime and Kelvin timelines merge into one and I only think that way because the fact the trailer was actually damn good this time around.
