How I would have handled Star Trek Into Darkness and future movies. For the most part I would keep Into Darkness largely the same until the end. Kirk would still die to save the Enterprise and crew, however the Vengeance would not crash and Khan would escape with the very powerful and deadly dreadnaught. Bones spots the tribble coming back to life and realizes they need Khan's blood to save Kirk. Hastily repairing the Enterprise they give chase as Khan revives his "family" with the goal of taking the fight to the Federation and making his family rulers again. END INTO DARKNESS.

Next movie would see the Enterprise with most of their battle damage repaired searching for Khan close to Klingon boarders while dealing with their feelings and worries that they might not find Khan or be able to save Kirk. There we find Khan has gotten a few Klingon ships on his side promising them his help in conquering the Federation and forever securing high honor and standing in the Empire. Together they attack the Enterprise under Spock's command and (keeping the trailer fodder) the Enterprise is destroyed to take out Khan, the Klingons while saving the crew. Vengeance is destroyed and crashes with a warp core breach that will blow in a about a weeks time with no way to stop it (ticking clock scenario) as well as all the Klingon ships save one (an up scale Bird of Prey) that crashes further off from the Enterprise upon the planet (seen in trailer, minus population) . Together they must find one another while fighting off Khan's genetically engineered family, Klingon survivors trying to repair their ship to escape and Khan himself. Spock goes after Khan, gets a bit of his blood and Bones is able to bring Kirk back in what remains of the Enterprise. (turning death into a fighting chance to live) All together the crew pulls together and beats Khan to the Bird of Prey and they take control. Sadly, in the process Carol Marcus is killed by a Klingon commander in front of Kirk stating how Klingons would never tolerate suck a weak race that relies on others. Kirk fights the commander and is left shaken by the loss. Vengeance blows, leaving the planet to become a harsh wasteland and Kirk chooses to leave Khan there, barely alive. (hinting towards future real Wrath of Khan) END BEYOND DARKNESS, NEXT MOVIE.

Returning home in their stolen Bird of Prey they are updated with a warning from Starfleet, while they've been away something unknown has been making it's way through Klingon space (maybe even obliterating the Klingon home system) on a direct course for Earth. Kirk, still hurt by the loss of Carol chooses to go after it, they catch up with it and find it to be a HUGE probe (Enter V'Ger story) that calls out to 0718 (the cyborg crewmember on the bridge) and is able to communicate with it. V'Ger would still be this huge, vast information gathering machine that does not see carbon based units as true life forms. Kirk is dead set on destroying it and is infuriated when and energy probe searches through his mind and recreates a humanoid probe Carol to study carbon based units aboard the ship. Spock calms Kirk down, having lost his world and his mother he understands such deep and hurtful loss. Together they come out stronger friends and come up with a plan to get close to the center of the probe. They find themselves inside the probe being taken closer and closer to Earth. Ships in the way are disabled as V'Ger comes closer. Surprise, surprise they find it to be a lost Voyager probe and it demands to speak with the Creator. They give V'Ger humanity through a mind meld between Kirk, Spock and V'Ger and V'Ger ascends higher. The Bird of Prey lands on Earth where they are greeted by a happy saved population. Kirk is promoted to Admiral and says farewell to Carol at a memorial erected to those who lost their lives before boarding a shuttle to a new ship he has been given commend to. Enter NCC 1701-A, and they all warp back off to explore the galaxy. "Let's see what she's got." NEXT MOVIE

We open with a lone Vulcan ship being attacked by and unknown ship, the Vulcan ship is crippled by a massive hull breach that blows the crew out into space. Two space suited shapes board the stricken shi and begin to pull data on a secret project "Genesis". They return to the mystery ship we come to find is commanded by Romulans and they tell their captain that the data was not complete. The Captain turns to a shadowy figure and says "We only have a few more days, I never should have taken you-" the figure cuts him off and speaks "There is another way" Cut to the Enterprise in orbit around a barren world, close to the Klingon boarders. There we find a secret hearing of Starfleet Admiralty and Captains to discuss allowing Klingons into the Federation after the events of the V'Ger probe having decimated their home system. Without support they would be doomed to extinction. Spock shows his full support, as it would be logical and the Vulcan people having survived this situation it would be ideal for them to join with the Klingons to help them both survive. It is then revealed that the planet they are one was a test for the Genesis device that would make worlds habitable in a matter of days. Kirk still has distrust and anger towards them after Carol's death, saying that all the pain they have caused across over several worlds and now they are just going to give them worlds to grow powerful again. Spock stands by his logic, saying that all can benefit while giving both Klingons and Vulcans a chance to have worlds of their own again. Kirk gives in and agrees to have the Enterprise escort a Klingon ambassador to Earth for the peace signing and transport of the full Genesis data and two working devices. On the way, the Enterprise's crew loses control and the ship begins firing upon Klingon ship. The Klingons fire back and both ships are disabled by perfectly controlled shots as if both knew exactly where to hit the other. The Mystery Romulan ship decloaks and orders the Genesis device be given over to them. Kirk refuses but is cut off as the Shadowy figure comes onto the screen and sends a data signal to the Enterprise which forces the ship to transmit it's data. The figure steps forth to show Khan aboard the Romulan ship. He explains that he was the last one alive, watching his family die as the planet became unlivable. A Romulan scout found him and took him prisoner. He explained who he was and what he knew with his knowledge of section 31 and would help the Romulans gain total dominance if they would help him get revenge. Using his knowledge of both Federation and Klingon secrets they sent spies into both the Federation and Klingon commands, first trying to destabilize the Klingon/Federation relations until they learned of the Genesis device, and whoever held such power could hold a weapon of unimaginable destruction while adding influence to the galaxy. Khan is intent on taking everything Kirk values away from him by destroying Starfleet and letting him watch everything around him die as he had suffered when Kirk left him. Khan then tries to beam over the Genesis devices but the Klingons who had been watching regain some control of their ship and ram the Romulan ship and interrupt the beaming as the Klingons escape their ship in shuttles, warping away. This gives the Enterprise a chance to limp away and hide as they make repairs. We see Khan starting to lose control, radiation from the planet he was stranded on is revealed to be killing him and he is becoming more irrational, fixated on Kirk and his revenge. The Romulan commander wants to leave the Enterprise, already having the data they need they don't actually need the other devices. Khan kills him and take full command of the Romulan ship, once able he goes after the Enterprise. Kirk spots Khan after him, he orders the Enterprise into a nearby nebula where they would be able to hide. Spock notices Khan's behavior, while brilliant is singled minded and suggests that Kirk may be able to make his lose focus by emotionally compromising him. (referencing the first movie) Kirk then begins to taunt Khan as he enters the nebula. Kirk tries to get the jump on Khan but is in fact tricked himself, but not before both get crippling blows off against one another. Khan beams over one of the Genesis devices before his ship's transporter gives out. He then arms it and threatens Kirk with it. Kirk then orders the other one armed, bringing both to a stalemate for a brief moment before Khan, calling Kirk's bluff begins the count down. Kirk tries to get away, but he knows it the Enterprise is too damaged. At the last moment, several Klingon and Vulcan ships enter the nebula having been told what had happened by the surviving Klingon Ambassador and had been searching outside but were unable to find them due to the interference until the massive energy signatures of the duel Genesis devices become active. With a combined effort they pull the Enterprise out away before the device detonates taking Khan with it. In the aftermath a whole new planet has formed, the Vulcans and Klingons agree to share the planet together in the dawn of a new age of peace and not use or pursue any more Genesis devices. The Enterprise is repaired around Earth and is seen returning to her mission of exploration once more.

>>>>> Keep in mind there is a LOT of room of character development and humor and undouble actiony scenes, this is just a basic plot outline of how I would have gone about with the Star Trek Reboot. There could still even be room for more movies. I personally feel a whole movie could be made with The Doomsday Device.