Season 3
01. The Battle for Cybertron (1)
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02. The Battle for Cybertron (2)
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03. The Battle for Cybertron (3)
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04. The Battle for Cybertron (4)
The Autobots consider the battle won until the Decepticons show a weapon to steal the allspark.
05. The Loop
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06. The Dead End
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07. The Sleeper
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08. The Citizen
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09. The Trial
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10. The Prisoner
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11. The Scientist
Hot Rod and Soundwave team up to battle a Quintesson scientist.
12. The Alliance
The Autobots and Decepticons team up in a last-ditch effort to save the universe from the Quintessons.
13. The Judge
The Autobots and Decepticons discover the terrible secret behind the Quintesson menace.
14. The End of the Universe (1)
The Autobots and Decepticons combine their forces to defend Cybertron from its impending judgement.
15. The End of the Universe (2)
With Optimus missing and the Quintesson Judge having captured the other Cybertronians, Windblade and Maccadam prepare their last resort.
16. The End of the Universe (3)
Cybertron bears witness to a clash of Titans.
17. The End of the Universe (4)
With no way left to fight a Quintesson-controlled Croaton, the Cybertronians are saved by an unexpected arrival.
18. Enemy Line
In an attempt to locate a missing Windblade, Bumblebee goes on a spying mission in Decepticon territory.
19. Thunderhowl
In their search for Windblade, Bumblebee and Chromia discover secrets hidden within the legendary Crystal City.
20. Wild Wild Wheel
A forgotten Autobot returns to Cybertron, searching for revenge.
21. Alien Hunt! With Meteorfire and Cosmos
To help Windblade, Bumblebee finds he must travel to Cybertron's forbidden moon.
22. Journey to the Valley of Repugnus
The search for Windblade continues as Grimlock joins Bumblebee on a journey to prehistoric Cybertron.
23. Rack 'n' Ruin 'n' Ratchet
A rescue mission to save Jetfire reveals a secret Decepticon operation.
24. Dweller in the Depths
Bumblebee and Chromia's search for Windblade takes them into Cybertron's gaseous Argon Sea.
25. Silent Strike
Optimus Prime leads a strike team of Autobots on a mission deep into Decepticon territory to destroy a dangerous artifact.
26. The Other One
In the series finale, the Autobots and Decepticons face the Other One, a powerful version of Megatron from an alternate universe.