What If JJ had made a big screen version of Space Seed instead of Wrath of Khan?
NuKirk's Enterprise is out on patrol and finds the SS Botany Bay. Kirk, and McCoy go over and wake Khan (played by a British Asian actor), who is disoriented. Kirk and him talk, Khan asks for reading material which Kirk provides. The 72 surviving Augments are recovered but not revived. The Botany Bay is taken into tow. Marla McGivers, a historian on-board falls for Khan and give him more technical material. While digging into the Botany Bay's primitive computers with Scotty, Spock comes to realisation that it's from 2036 (NuTrek shifts the dates a little) after the Eugenics Wars - cue flashback- a series of Earth Wars from 2030-36 vs genetically Augmented Superhumans who had seized power in 40 countries. Khan in charge of an expanded India was regarded as the most rational and stable, his regime actually worked, even he was part of the war defending the lands he had seized. Then in 2023 he vanished along with 76 followers. The SS Botany Bay has no record, but matches the ships launched by India/EU at the time. The Eugenics Wars lead to the instability that caused the rise of ECON and World War III in 2040. Spock's findings make sense of the amazing medical scans McCoy did of Khan and the still frozen others.
Kirk confronts Khan who does not deny whom he is. Kirk contacts Starfleet Command for instructions. Khan is charming, persuasive, and woos all the crew he comes into contact with including the young Chekov- it is implied he gets into bed with some of them. Khan is learning at a ridiculous rate and is seen doing things with various 'household' objects in his quarters, and programming on tablets. Eventually Khan persuades Nurse Chapel to show him his frozen crew mates- Khan proceeds to do something to one of the pods, and they leave. As we see Khan in the mess telling stories to a circle of admirers the pod opens and a young Augment- Joaquin gets out- he finds a tablet Khan has left and reads instructions from his Leader- then starts opening the other pods. An Enterprise security team comes to investigate, but Joaquin kills him. Now they are armed.
Khan requests to see the senior crew and in the briefing room outlines a plan to allow him and his people to settle on a remote planet since it is clear to him there is no place for Augments in the modern Federation. Kirk, Spock and the others debate this. Khan asks them to think about it and leaves. Just after he goes Red Alert is sounded and a panicked Chekov says the Bridge is under assault, and they have no contact with the engine room. Kirk goes to leave the room and finds the door locked and security overwritten. Enterprise changes course- from the room's computer Khan is heading for Earth. It takes some time, but Scotty gets them out and heads for Aux controls with Spock while Kirk heads for the Bridge. McCoy returns to Sickbay.
In Sickbay McCoy comes across a makeshift tube in which McGivers is suspended- Khan has given her a nutrient bath to Augment her based on his and the other Augments fluids. McCoy gets her out, but McGivers attacks him for stopping 'the process' forcing McCoy to knock her out. Spock and Scotty fight their way to Aux Control- Vulcan strength proving a good counterpoint to Augment abilities. As suspected the Engine Room is heavily guarded, as is the Bridge. Scotty warns Kirk and floods the Bridge with gas which knocks out the Augments, but not before Otto warns Khan and Kati. The latter is holding the Enterprise crew hostage and as she and others are distracted with the call Sulu goes for her- unleashing a flip out sword and taking her on while other Enterprise crew take on the other Augments. Kirk heads for the Engine Room instead.
Kirk, and Spock reach the Engine room and try to reason with Khan who gives a powerful speech about how 'Humanity has not changed' and 'are not worthy' etc; kirk and Spock are joined by a battered Sulu and some crew including Andorians, and Vulcans- they have got Security armour and phaser rifles. The Battle for Engineering is joined. Khan lets his people lead with it while he attempts to override the lockouts Scotty has placed on the controls- he will have his revenge on Earth by ramming Enterprise into the planet at warp!
Spock holds off Augments allowing Kirk to go at Khan, who easily brushes him off. Keenser appears behind Khan and bends over allowing Kirk to push the superman over, giving Keenser an advantage to slap a transporter badge on him- Scotty then beams Khan into the Brig. Spock nerve-pinches Joaquin and the other Augments are defeated by the crew. In the Aftermath Kirk stops the ship and repairs are started.
Kirk is briefed by Admiral Pike- Starfleet Command is at a loss as to what to do with Khan, some want him to answer for his crimes, but others are afraid of the shitstorm that will kick up about Augmentation and how it might help Humanity. Others want to tap his intelligence to help Starfleet to build better weapons and ships. Kirk outlines Khans own plan for dropping them into a system with the basics. Surprisingly, Pike agrees that might be for the best. Kirk has Spock find somewhere out of the way, and he comes across Ceti Alpha V. Kirk informs Khan he is to be left there, an offer which Khan accepts quoting Milton's Paradise Lost that "it is better to rule in Hell than to serve in Heaven." Several of Enterprise's crew who helped Khan's people such as McGivers and Chekov are given the choice to go with him or face a court martial. Chekov takes his lumps, but the semi-augmented McGivers wants to be him 'her man' and goes.
Captain Kirk leaves them with on the Paradise world with a ton of supplies, and basic building tools. The Botany Bay is left in orbit of the moon. Enterprise warps away. Spock speculates they will have to come back in 50 years to see what Khan has built.
Post credits: Khan pulls out a communicator and contacts Rodriguez on the Botany Bay, who confirms he got want they wanted. Khan smiles, and the screen shows the old ship full of phasers, transporter patches, armour, space suits, misc. crates and multiple tablets of data...