As Megatron fakes his death for using Omega Supreme, Shockwave, Lugnut and Blitzwing start a breakout at Cybertron. Bulkhead returns to his Energon farm when the decepticons attack, and ends up kidnapped. And all his friends are getting absorbed into Megatron into a Marauder form. Then he starts attacking the Autobots, and now Optimus Prime (still in control of Ultra Magnus' hammer), Bumblebee (now an elite guard and married to Arcee), Ratchet, Arcee joins the Autobots, Jazz (replacing the deceased Prowl) and Ironhide (replacing Bulkhead) will have another chance to stop him again with the help of 15-year old, Abigal Witwicky, niece of Spike and Carla Witwicky.
- Optimus Prime (Voiced by - David Kaye)
- Ratchet (Voiced by - Corey Burton)
- Ironhide (Voiced by - Corey Burton)
- Arcee (Voiced by Susan Blu)
- Jazz (Voiced by - Phil LaMaar)
- Bumblebee (Voiced by - Bumper Robinson) is now elite guard and married to Arcce.
- Blackaracnia (Cree Summer) - reforms when she realizes that Sentinel Prime and Megatron are the same thing and fixed the past!
- Spike Witwicky (Corey Burton) - partner to Bumblebee
- Carly Witwicky (Tara Strong) - Spike's wife and partner to Arcee
- Daniel Witwicky (Tara Strong) - Spike and Carly's son
- Nancy Witwicky (Candi Milo) - Daniel's 4-year old sister
- Sparkplug Witwicky (John Mariano)
- New Characters:
- The Fallen (Voiced by - Jonathan Adams)
- Sideswipe (Voiced by - Neil Ross)
- Kup (Voiced by - Edward Asner)
- Unicron (James Earl Jones)
- Primus (James Earl Jones)
- Vector Sigma (Wally Wingert)
- Megatron (Voiced by - Clancy Brown) - revealed to be Sentinel Prime, he planned on changing the Past to gain power over Cybertron, and made a deal with Ultra Magnus by giving him a chance to rule Cybertron by allowing Megtron to be his successor!
- Shockwave (Voiced by - Corey Burton)
- Blitzwing (Voiced by - Bumper Robinson)
- Lugnut/Tankor (Voiced by - Kevin Michael Richardson) - transformed into Tankor thanks to Dark Energon!
- Starscream (Voiced by - Tom Kenny) - trapped as Megatron's slave under the Dark Energon
- Cyclonus (Voiced by - Liam O'Brien) - lost his cowardness as Skywarp and became more evil as Cyclonus thanks to Megatron with the Dark Energon
- Scourge (Voiced by - Jim Cummings) - once Thundercracker, now Scourge with his Sweeps
|43||The Trial of Megatron, Part One||September 7, 2012||Sari wants to learn more about her origins, Sentinel tries to become Magnus, Bulkhead's hometown is targeted by Decepticons, Megatron relocates Kaon to Earth using his trial as a distraction, and there is a spectacular prison break.|
|44||The Trial of Megatron, Part Two||September 7, 2012|
|45||The Trial of Megatron, Part Three||September 7, 2012|
|46||Allspark-alypse Now||September 14, 2012||Sentinel comes to Earth and intends to use the AllSpark to kill Megatron, as Prowl's ghost inhabits Cybertronians powered by AllSpark fragments, telling Optimus about the consequences of Sentinel's ideas.|
|47||S.T.E.A.M.||September 21, 2012||The Autobots are forced to save their detractors when the steampunk tool-using, anti-technological Luddites of "Save The Earth And Mankind" run afoul of Soundwave.|
|48||Mirror, Mirror||September 28, 2012||Bulkhead and Sari enter a mirror universe with evil Autobots and heroic Decepticons.|
|49||Gremlins in the Gear||October 5, 2012||The Minicons who run Kaon disassemble all machinery in Detroit, while Ratchet and Fanzone have to stop it.|
|50||It Came from Planet Cybertron||October 12, 2012||Cosmos has an important message for Optimus, and comes to Earth to tell him. He loses his memory after scanning a prop flying saucer from a B-movie's set, and hi-jinks ensue.|
|51||Turf War||October 19, 2012||The Constructicons battle with the Decepticons over control of the energon in Detroit.|
|52||Megatron Must Be Destroyed!, Part One||October 26, 2012||Megatron's machinations threaten the entire planet. Optimus gathers as many allies as imaginable to defeat Megatron once and for all.|
|53||Megatron Must Be Destroyed!, Part Two||October 26, 2012||
Optimus realizes that Megatron and Sentinel Prime are the same person, when he realizes Ultra Magnus's betrayal and using the Chronosphere to alterate Time, Sentinel was defeated with the aid of Blackaracnia who realizes the Spiders was a scheme to let Optimus take the fall, at the end Megatron leaves crippiled with Starscream, and Ultra Magnus was forced to be the Space Bridge Builder head, and Optimus takes his rightful place as the true supreme Commander of the Autobots with Blackaracnia as second in command!