this is what I wrote on another board back in 2011 when no one really knew what was going on with Khan (back when it was rumoured the villain may or may not be Khan)
see how it faired against what eventually happened (better/worse)
see how it faired against what eventually happened (better/worse)

another Federation vessel (Reliant) led by Captain Matt Decker (stephen Collins) finds the botany bay and gets totally POWNED by Khan who kills everyone and steals the ship (basically what wouldve happened in Space Seed had Khan not picked on Captain Kirk - and obviously what did happen in The Wrath of Khan)
Khans federation ship venters into klingon space and is attacked by klingons scout ships, Khan destroys them and captures a klingon BOP which he then comendeers (shades of Star Trek III and the 'Enterprise' augments episodes) and then uses it to attack Federation ships/colonies - inciting a war between the federation and the klingon empire (kind of like Star Trek VI in that respect as well as the 'Enterprise' augments 3 parter)..his ultimate aim to have them wipe each other out so he becomes ruler of the galaxy. (lots of talk about destiny, how they fled earth for this purpose etc)
Kirk and crew are given the task of sorting it all out against a back drop of epic space battles (Federation ships vs klingon cruisers and BOPs, Enterprise vs Reliant etc), possibly include some Genesis/red matter style mcguffin, intrigue/ mystery/twilight zone eeriness, discovering who khan is, subtle hints that this has all happened before and differently (possible Nimoy cameo) - eventually revealing to the Klingon High Command that Khan is behind it, ends with Kirk and Khan finally confronting each other and engaging in an epic fight, Khan eventually marooned somewhere (not killed)
so itd be kind of 2 villains like in The Dark Knight - Khan who is a nutjob psycho causing a heap of trouble (joker) and Klingons who arent that aggressive to the Federation at the start but due to khan stirring s**t up become a really formidable enemy (Harvey Dent)
all plays out differently to Space Seed and TWOK (but with the odd similarity/homage) - no Khan wanting revenge against kirk etc so it wouldnt really be another khan like villian out for revenge (which is what Nero was), no Genesis, maybe throw Carol Marcus in there as Kirks love interest. Familier klingons like Kor, Kolath, Kang, Kruge, etc. Have the ‘No Country For Old Men’ bad guy as Khan. Plus get some A list stars to boost popularity and box office overseas - Arnie as the Klingon Emperor? Harrison Ford as the head of starfleet? Russel Crowe as Kruge? Reese Witherspoon as Carol Marcus?
regarding Khans origins - maybe have a flash back scene or even a prologue showing him created/Eugenics wars in the 1990s - interesting dilema of how to handel the 1990s issue with canon etc - maybe just mention it but not be time specific...i.e. it happened sometime in earths past and let the (non trekkie) audience assume its sometime in the 21st century (post 2012) but have nothing to suggest it wasnt the 1990s (so as not to upset us fans whod scream 'CANON VIOLATION!')…like in the Enterprise Augments 3 parter (even Khan is mentioned) but no mention of the actual year……or as in the Greg Cox books have Khan and TEW as having happened discreetly (as we know the novels do sometimes influence on screen canon). Could probably delve into the origins of the klingons too (as theit origins havent really been touched upon in any series) also the Klingons could find out the DNA that caused their race’s mutation is the same DNA in Khan and his people (see 'Enterprise' season 4) therefore causing further friction (funnily enough early reports about The Wrath of Khan erroneously said Khan was leader of the klingons....plus in Trek II khan mentions the old klingon proverb...maybe that was a prelude to a tantalising glimpse into another reality where he is their leader or adversary?)
and to those who say “meh no Khan as its been done already/it lacks originality/go with something totally new etc’..well then why bother having Kirk and Spock etc in the new films either? – dosnt that show a lack of originality? – the star trek universe is a big place, surely they couldve/shouldve gone with an all new crew on a new ship….
Wrath Of Khan is the most popular, enduring ST movie of them all. the template that most of the other movies followed so itd make sense to capitalise on Trek 09s success with the most recognisable/popular villain for the sequel, done a new and different way - like TDK did with the joker or Sherlock 2 with Moriarty, or ST FC with the borg - ST09 was sort of taking its cue from the Batman reboot(set up main character(s) with not so well known villain so no overshadow the main characters introduction) so id expect them to follow doing similar stuff with the sequel (I.e. hit everyone with the most well known villain for the sequel - in the ST09 dvd commentary they even said there was a Botany Bay ending discussed - which wudve been very sim to the joker card in BB. It showed Khan was on their minds anyway). Why bother saving Khan for a 3rd or 4th when if the 2nd isn’t that great - dosnt engage audience due to weak villain etc there might not even BE a 3rd or 4th. Also Khan hasn’t been exactly overused - 1 episode and 1 movie - and it cant be the madman TWOK version of Khan out for revenge anyway (which is pretty much what Nero was)
i guess they could do klingons only for star trek ‘2' and set Khan up for the villain for Star Trek ‘3' (something similar to the way the joker was set up at the end of Batman Begins) but itd be much better if the combined them into one movie and focus on another classic villain for the 3rd film in 2015 (e.g. the borg )
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