This is how the Megatron timeline and Thomas escapes from Megatron goes in Sci-Ryan's and Clay's Time Travel Adventure.
[Ryan, Thomas, Crash, Sci-Ryan and Clay come out of the time portal and saw everything on Earth has been in ruins]
Ryan F-Freeman: Oh no.
Thomas: Come on. We need to find out what happened.
Sci-Ryan: Looks like everything is ruined. Game over man!
[Thomas sees some kind of fortress in the distance]
Crash Bandicoot: Look. There's shelter.
Ryan F-Freeman: I'll take it from here. [slices the Cons to bits]
[But they keep coming and Soundwave grabs them all]
Ryan F-Freeman: Soundwave? You remember me? Ryan?
[Soundwave shakes his head and takes them to the fortess. At the top he produces them to Megatron]
Sci-Ryan: Megatron? I thought you were a good guy.
Megatron: No. Crystal Prepper. I'm not the Megatron who you speak of. You and your friends came here with some kind of ability to travel through time.
Ryan F-Freeman: Wait! What happened to this place!? It looks like a fiery wasteland!
Megatron: I think you mean Wonderland.
Sci-Ryan: Not for us. We have to find a way to go back in time and stop a jester from changeing the past. I know that if Matau eat a ladybird in the past, it can alter the present.
[Ryan tilts his head]
Thomas: It's either that or Ryan will be fighting dinosaurs.
Ryan F-Freeman: Cody would love them. But, everything here are gone. From trees to unlimited rice pudding.
[Sci-Ryan laughs because Ryan said "Unlimited rice pudding"]
Megatron: Am I seeing 2 Ryans?
Sci-Ryan: Yeah. But this Ryan used to be a human.
Ryan F-Freeman: Oh, Optimus should've killed Flash Fire when you had the chance.
Crash Bandicoot: What about Sunset? Is she with you?
Megatron: That organic means nothing to me. But, she's my queen.
Ryan F-Freeman: Optimus and Twilight. We saw Prime ok in our timeline.
[Ryan gets a vision]
Optimus Prime: In order to both protect the Allspark and secure Unicron's defeat, it was necessary for me to empty the vessel's contents.
Thomas: Into where?
Optimus Prime: The Matrix of Leadership and Ryan's spark. As such, my own Spark can no longer be separated from the multitude of others within me. And the very same thing has happened to Ryan.
Ryan F-Freeman: Yeah. Sorry, Twilight.
Princess Celestia: Ryan...
Princess Luna: You're not going to say...
Princess Cadance: You're leaving us?
Twilight Sparkle: [sadly] Optimus? You sold me out?
Ratchet: Are you telling us that you and Ryan are now one with the Allspark?
Smokescreen: That's what you say when someone kicks the.
Ultra Magnus: To not return the Allspark to the well would be to prevent future generations of new life from existing on Cybertron.
Optimus Prime: My quest must be completed without Twilight.
Sci-Ryan: Does this mean the connection between the Matrix of Leadership and the Element of Magic is no longer in effect?
Ryan F-Freeman: Yes. That's really what it means.
[Ryan hits himself ending the vision]