The Unicron Trilogy (2002–2006)
Main articles: Transformers: Armada, Transformers: Energon, and Transformers: Cybertron
These three lines, launched in 2002 and dubbed the "Unicron Trilogy" by Transformers designer Aaron Archer, are co-productions between Hasbro and Takara, simultaneously released in both countries, each lasting 52 episodes. Armada followed the Autobots and Decepticons discovering the powerful Mini-Cons on Earth, which are revealed by the end to be weapons of Unicron. Energon, set ten years later, followed the Autobots stopping the Decepticons from resurrecting Unicron with energon.
In Japan, the series Transformers: Cybertron showed no ties to the previous two series, telling its own story. This caused continuity problems when Hasbro sold Cybertron as a follow-up to Armada/Energon. Plot elements have been changed from the Japanese story into references to the previous shows to enhance continuity, but they largely only add up to mentioning Unicron once or twice.
Just as Marvel produced a companion comic to Generation One, Dreamwave Productions published a comic entitled Transformers Armada set in a different continuity to the cartoon. At #19, it became Transformers Energon. Dreamwave went bankrupt and ceased all publications before the storyline could be completed at #30. However, the Transformers Fan Club published a few stories set in the Cybertron era.