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When a small space bridge repair crew, consisting of Optimus Prime, an idealistic former Autobot Academy guard, Bumblebee, an energetic hotshot, Bulkhead, a large wrecking-ball wielding worker, Prowl, a ninja-like loner, and grumpy Cybertronian War veteran and medic Ratchet find the Allspark amongst the meteors when clearing a space bridge in an asteroid field, they also find a ship of Decepticons looking for them. Heading back to Cybertron, their Supreme Commander Ultra Magnus is unconcerned with the threat of the Decepticons, but tells them not to play at being heroes. The Decepticons led by Megatron attack to claim the Allspark.

Season 3 Episode 13 – Endgame, Part II

In the Season 3 finale, the Autobots battle against the Decepticons in the ultimate showdown.

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Season 3 Episode 12 – Endgame Part 1

The Autobots discover Arcee's energy signal on the Moon. Rachet insists on going there right away to save her, but Prime refuses, knowing that they are too weak to fight Megatron. Rachet, Sari and Professor Sumdac build flight boosters for Optimus to even the chances. Prowl tries to put the Allspark back together, using processor over matter. Meanwhile, Shockwave finally gets Arcee's codes and uses it on protoforms (stolen by Starscream, to make his clones) to duplicate Omega Supreme. Finally, Omega Supreme's clones fly from the Moon to invade the Earth. The episode also shows some of Optimus Prime's memories about being expelled from Elite Guard and meeting the other main characters.

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Season 3 Episode 11 – This is Why I Hate Machines

Ratchet activates Bulkhead's Space Bridge, which ends up sucking Captain Fanzone into it with Ratchet following him. They both end up on Cybertron around the time Sentinel Prime has declared a lockdown. Omega Supreme has arrived on Cybertron with Megatron, Starscream's Head, and Lugnut; thus, Shockwave, still posessing Ultra Magnus' hammer, attempts to get Omega's access codes from Arcee herself.

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Season 3 Episode 10 – Decepticon Air

The Space Bridge on Earth is finished. Meanwhile, the Elite Guard ship holding most of the Decepticon prisoners heads straight into an ominous space storm. The space storm reactivate Swindle who frees the Decepticon prisoners and takes over the ship. Optimus Prime identifies the "Broken Lance" code from Sentinel Prime and uses the Space Bridge to transwarp to the ship. The title may be a reference to the movie Con Air which has a similar plot.

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Season 3 Episode 9 – Human Error, Part II

It turns out that Soundwave has trapped the Autobots in a virtual reality intending to brainwashing them to his way of thinking. Now, Sari must free them before Soundwave completely turns them into Decepticons. She leads a ragtag team of allies - Snarl, Scrapper, and Wreck-Gar - into battle against the Autobots.

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Season 3 Episode 8 – Human Error, Part I

On Christmas Eve, Optimus Prime patrols the city in search of Soundwave. With Porter C. Powell selling Soundwave action figures, Optimus is paranoid that the real Soundwave is out there. When the Autobots drift off to sleep, they awake as full fledged humans. Now they must figure out what happened to them while dealing with a Decepticon onslaught.

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Season 3 Episode 7 – Predacons Rising

The Autobots and the Elite Guard pursue Wasp for their own agenda for Wasp. However, Blackarachnia has Swoop capture Wasp in her latest attempt to get rid of her organic half. Jetfire and Jetstorm attack the Dinobots so Sentiel can get in, learning of Elita's fate while Wasp emerges as Waspinator. Optimus and Bumblebee arrive as Waspinator realises Blackarachnia used him and attacks her, the transwarp energy inside him going critical. Though the Primes refuse to let her go again, Blackarachina sacrifices herself by covering herself and Waspinator in a web cocoon so the blast can effect only them while the ensuing explosion takes out a chunk of Dinobot Island. As Sentinel and Optimus finally move on as Sentinel's group returns to Cybertron to deal with the chaos there, Blackarachnia survives and finds herself and the disembodied Waspinator in the jungle surrounded by a group of animals.

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Season 3 Episode 6 – Five Servos of Doom

A crazed Wasp finds his way to Earth to exact his revenge on Bumblebee... but he doesn't count on the Elite Guard following him. When Wasp swaps bodies with Bumblebee, Bumblebee must try to convince the Autobots and the Elite Guard who he is. At the same time, Optimus Prime tries to convince Sentinel that Longarm Prime is actually the Decepticon Shockwave. In the end, it is revealed that Shockwave severely wounded Ultra Magnus in an attempt to make sure his identity as a Decepticon spy doesn't get revealed.

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Season 3 Episode 5 – Where Is Thy Sting?

Unaware that he is being followed by the Elite Guard, Wasp heads to Earth to take his revenge on Bumblebee.

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Season 3 Episode 4 – Three’s A Crowd

Bulkhead must face off against the Constructicons and their new leader, Dirt Boss, when they decide to hold the city's oil supply hostage. Meanwhile, the other Autobots manage to capture Lugnut, but find hauling him away a more difficult task.

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