-Knockout is kidnapped by MECH, who actually remain exactly the same as we know them. He's basically placed in the same situation the Breakdown the Autobots already know was (right down to the optic removal)
-Starscream is terrified of med bays, because early on in the war, he was kidnapped by the Autobots and brought to one of their labs (which was a converted med bay) and opened up to 'see what made him tick'. He was rescued by Megatron, but the trauma remains
-Starscream does NOT want to kill Megatron and replace him as leader
-SG!Smokescreen is the parallel to the Starscream we know, in that he wants to lead the Autobots
-Shockwave and Ratchet work together to help the Autobots find a way home
-Upon the Autobot's departure:
Optimus: "It is reassuring to know that, though in another dimension, the Megatronus I once knew still lives."
Megatron: "I could say the same of you, Orion."
And then, ideally, a sequel where the SG!Decepticons (or at least a few, being Megatron, Soundwave, Starscream, Knockout, and Breakdown) end up in the Prime!verse we know. The Autobots bring them to their base, freaking the kids out until everything is explained to them, though they're still wary of the SG!Cons. These Decepticons then help the Autobots defeat THEIR counterparts. Eventually, the SG!Decepticons find a way to transport themselves back to their own dimension (very specific requirements that they thought they wouldn't be able to recreate caused the Autobots to return to their own dimension before), but they manage to configure it so that they can travel to and from at any time. When the Decepticons go to leave, Miko tries to follow, but is pushed back by one of Soundwave's tendril...things... to keep her from coming with them.
Points if Starscream gets kidnapped by the Decepticons of the Prime!verse and they decide to see if there's a significant difference, so they begin to open him up before he's able to be rescues. He's practically catatonic due to fear and resurfaced memories by the time they get him back to base