Here is how the Villains capture the Heroes and traveling to the future goes 3 weeks later in Thomas and Twilight Sparkle join Overwatch.
(3 weeks later)
(Our Heroes are relaxing)
Brian Griffin: This is the best relaxing day, ever.
Peter Griffin: Agreed.
(Suddenly, the villains appear)
Diesel 10: Hello, everyone!
Our Heroes: The Villains!
Queen Chrysalis: (lands) You got that right!
(The other villains surround them and capture them, except for the Autobots)
(They then lock the heroes in a cage on Lockdown's ship)
(Later, in the cockpit)
Queen Chrysalis: Finally, we have them in our grasps.
Adagio Dazzle: They won't get away from us now.
Lockdown: Initiate dark matter drives, full power!
(Some of Rourke's men get to work on the engines)
Tirek: This is the perfect time to test the time warp device.
Lockdown: No, it's too dangerous. We've never tested it on anything.
Megatron: We leave them in a different time, we take over the universe.
Starscream: It's worth a try.
Lockdown: (looks at a technician and nods)
Technician: (nods back and heads to fire up the time warp device)
(Meanwhile, Cade, Optimus, Bumblebee, Ironhide, Ratchet, Sideswipe, Dino, Mudflap, Skids, Arcee, Brains, Wheelie, Drift, Hound, and Crosshairs enter the ship)
Cade Yeager: I never thought we'd be back here again.
Optimus Prime: Me neither.
Cross-Hairs: Hopefully, we blow something up.
Hound: Those of you who have never been on here, Lockdown's ship has booby traps, eyes open.
Cross-Hairs: Beware of bone grinders, brain blinders, flesh peelers, chromosomal inverters, catatonic sludge, blackhole trap doors, and of course, radiation.
Drift: We have a map of the ship. We should look in the bigger cages. It's where they will be keeping the bigger ones.
(An alien tentacle tries to attack him)
(Drift begins to fight back)
Cross-Hairs: Ah, kill it! Kill it!
Drift: I kill you! Kill you! (kills it)
Cross-Hairs: Ugh, I hate those things.
Cade Yeager: Freaky.
Drift: It's not alive anymore.
Cross-Hairs: Well, we looked in this area, they're not here, let's move on to the next area.
Optimus Prime: Anyone who originally came to Earth, with me. We'll search the smaller cells. Autobots who were there for the Fallen or Chicago, search the larger cells. Cade, you and the others sabotage something.
Cross-Hairs: Let's go sabotage this nightmare ship.
(They split up)
(we then see Cade, Hound, Drift, and Cross-Hairs slowlly making their way through the ship)
Cade Yeager: They could be anywhere, so eyes open.
Hound: This place creeps me out.
Cross-Hairs: You and me both.