List of Transformers Animated Episodes - Season 3: 2009

Around the galaxy, Decepticons are battling the thin-spread Autobots' Space Bridges to join in Megatron's planned invasion from the previous season. Meanwhile, as Sari and Professor Sumdac deal with the fallout of her shocking discovery, the Autobots try to contact Cybertron to warn them of the traitor Longarm in their midst. Meanwhile, Megatron and Starscream inadvertently stumbles upon Omega Supreme's offline body, who they soon decide to use to conquer Cybertron, where an increasingly desperate Longarm/Shockwave tries to cover his tracks. Blurr escapes his confinement with the Starscream clones Thundercracker and Skywarp, and races back to Cybertron, only to be crushed by Shockwave.

While trying to recover spare parts from Megatron's Space Bridge with Bulkhead, Bumblebee is TransWarped to a far-flung region of space, and is consumed a by a rock-like alien, who transwarps back to Earth as well. When the Autobots go to save Bumblebee, Sari uses her Key to upgrade herself to help the Autobots, but soon she loses control of her body. She goes on a rampage and as Bumblebee tries to stop her, Sari accidentally stabs him in his chest-plate.Finally, Ratchet uses his EMP generator to knock her out. Bumblebee is rescued and Sari is left with a teenage body (16 years old), instead of a child body. Megatron arrives on Earth, but he and Starscream are soon sent on an endless Transwarp cycle inside Omega Supreme across the galaxy by the Autobots.

Bulkhead and Isaac Sumdac try to rebuild the Space Bridge that Megatron had built. When Bulkhead convinces the Constructicons to help out, a combination of a forklift, a Headmaster unit and an Allspark fragment gives birth to Dirt Boss. Meanwhile, the others track down any remaining Decepticons and run into Lugnut. Dirt Boss, having the ability to control other bots due to a mind-control drill, uses it to make Bulkhead go on a rampage. Optimus and the others come to help, leaving Lugnut alone. The end result is the Constructicons being transwarped to Dinobot Island, and Lugnut being freed and befriended by Ramjet – the Liar Starscream clone.

A crazed Wasp finds his way to Earth to exact his revenge on Bumblebee, but the Elite Guard follows him. When Wasp swaps places 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, Wasp escapes and Shockwave savagely attacks Ultra Magnus after his identity is revealed.

Absent: Sari Sumdac, Megatron, Starscream, Lugnut

Sentinel Prime has incredible success capturing fugitive Decepticons Sunstorm, Blitzwing, Swindle (who is still frozen in vehicle form), and Lugnut. This leads Prowl to suspect he's getting help. As he flashes back to his training under Yoketron, Prowl discovers that Lockdown is helping Sentinel for a price. Prowl ultimately defeats Lockdown, avenging Yoketron's death and regaining Yoketron's helmet as well as his upgrade armor in the process, but the bounty hunter escapes.

Absent: Bumblebee, Ratchet, Bulkhead, Sari Sumdac, Megatron, Starscream, Lugnut, Shockwave

The Autobots and the Elite Guard pursue Wasp, each with their own agenda. However, Blackarachnia has Swoop capture Wasp in her latest attempt to get rid of her organic half. Jetfire and Jetstorm attack the Dinobots so Sentinel 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, Blackarachnia sacrifices herself by covering herself and Waspinator in a web cocoon so the blast can affect 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 and Waspinator end up in the jungle. Waspinator tries to pull himself back together, while Blackarachnia finds herself surrounded by a group of animals paying homage to the beast forms of the core group of Maximals from Beast Wars.

Absent: Sari Sumdac, Megatron, Starscream, Lugnut, Shockwave

Porter C. Powell is selling Soundwave action figures on Christmas, and this has Optimus feeling a little uneasy. All seems well though until the Autobots wake up the next morning and discover that they have been turned into humans, and with the Autobots out of the way the Decepticons move in with a full scale invasion. All hope seems lost but when the Autobots are able to fight back with unrealistic power, the group discovers they are trapped inside a virtual reality by Soundwave, and now are faced with the challenge of escaping it.

With Soundwave having trapped the Autobots in a virtual reality, Sari must free them before Soundwave completely turns them into Decepticons. She ends up gaining unlikely allies in Snarl, Scrapper, and Wreck-Gar, whom she dubs the "Substitute Autobots". The group defeats the Autobots, freeing them from Soundwave's control, and Optimus destroys Soundwave's body; with Laserbeak soon afterwards flying off with Soundwave's core.

The Space Bridge on Earth is finished, whilst the Elite Guard ship holding most of the Decepticon prisoners heads straight into an ominous space storm. The space storm reactivates Swindle, who frees the Decepticon prisoners, allowing them to take over the ship. Optimus Prime receives a distress call from Sentinel Prime and uses the Space Bridge to transwarp to the ship, where he helps fight back against the Decepticons. Swindle and Lugnut escape the ship, while Blitzwing and the Starscream Clones are taken to Cybertron as prisoners; however, Lugnut finds Megatron and Starscream, and joins them inside Omega Supreme.

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 possessing Ultra Magnus' hammer) attempts to get Omega Supreme's access codes from Arcee herself instead of Ratchet to reprogram Omega Supreme. In the end, Ratchet steals Ultra Magnus' hammer back, Jazz joins Optimus Prime's team, and Arcee is shown to have at least some of her memory back.

Absent: Optimus Prime, Bumblebee, Prowl, Bulkhead, Sari Sumdac, Prof. Sumdac

The Autobots discover Omega Supreme's energy signal on the Moon. Rachet insists on going there right away to save him, but Prime refuses, knowing that they are too weak to fight Megatron. Ratchet, 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 the Elite Guard and meeting the other main characters.

The three Lugnut Supremes touch down on Earth and launch a full scale assault on Detroit. While Optimus Prime and Prowl fight the Lugnut Supremes and take one down, Ratchet, Bulkhead, Bumblebee, and Sari head to the moon to rescue Arcee and reactivate Omega Supreme; Starscream then takes over the remaining two Supreme clones and initiates their selfdestruction. Prowl begins to gather the Allspark fragments to block the explosion, including Starscream's fragment, killing Starscream for good. Failing to gather enough, Prowl sacrifices his Spark and makes an Allspark force field that surrounds the last selfdestructing Starscream Supreme. Megatron attacks one last time, but is defeated and arrested by Optimus. The Autobots have won, captured Megatron, Shockwave, and Lugnut, and returned to Cybertron with Prowl's body and several rescued protoforms that Master Yoketron (Prowl's Cyber-Ninja master) died protecting.