I'm not really expecting that this would be the story nor I would wish it were, but somehow if I did story it would go like this...

Sam is doing fine on his new job. Of all the concidences that would happen, he stumbles to an Allspark fragment and comes into trance this time to see the future. He see that all Autobots are dead and sees a robot walking among the smoke that covers the air and Shockwave shows up saying "They're all dead". Upon waking from that trance/dream Sam he goes back to work making himself busy and simply ignoring the vision he saw.

As it was confirmed that Shockwave would be the main villain, he wold come to earth to aid Megatron's quest to defeat Optimus Prime. However, Shockwave has other plans which is to be the TOP Con, so he plots to kill Megatron. They go on to battle against the undersized and outnumbered but valliant Autobots. The Autobots again gave the Decepticons a heck of fight. As soon as Megatron faces Optimus Prime, the former took a beating and here come Shockwave. Seizing the opportunity, Shockwave kills Megatron and this stunned Optimus. Shockwave leaves to retreat and told Prime that that is just the beginning.

Sam told Prime about what he saw and Prime easily confirms that that is the future. He then showed with hologram to tell their story about Alpha Trion's vision that Cyberton would fall. the Allspark can reveal the future to a selected few but somehow Prime told he was surprised that even the Allspark may reveal such vision to a human. Sam bursts into a state of denial that it won't happen.

Sam would happen to recall what he studied in school about the Pygmalion effect, and he discussed this with his Dad. And this would be recurring topic about other friends and/or people including Simmons. Simmons would just add fire by stating theories of probability and possibilities, and even quantum mechanics of tuning to different futures. Comically it would only add to Sams confusion.

Sam would meet decepticons on street again and again autobots to the rescue. Another scene, about the vision, then another fight, then another and another. blah! blah! blah!

Until the climax that Sam would experience De Javu. Seeing what he saw before. looking to all dead autobots and decepticons and the air filled with smoke and a tall walking robot going to him and it was Shockwave and then it says "they are all dead" and just as the scared Sam is getting more petrified having Shockwave's one eye gazing at him it turn to its back and left Sam.

then credits

there was a rocket to be sent to outer space in order to throw the remains of Megatron and toehr decepticons. All remaining Autobots at the station are talking with Sam talking about their future, that they will create their future as they see it. After that Megatron was floating in space but near an gargantuan object and it emitted an energy to drag his body to be near him ... it is <you know who>