Unicron stands as the overarching antagonist in Transformers: Armada. His origins stem from an ancient conflict ending in defeat by the Autobot Omega Supreme. Following this loss, Unicron concealed himself by assuming the form of Cybertron's moon, lying dormant while observing the Transformers' civil war.

He engineered the artificial Mini-Cons specifically to escalate hatred and conflict between Autobots and Decepticons, sustaining himself on the resulting energy. To manipulate events, he deployed agents like Sideways and Thrust. Sideways infiltrated both factions as an emissary, sowing discord and retrieving Mini-Con weapons, while Thrust orchestrated tactical schemes to intensify hostilities. Unicron remained hidden until the assembly of the three Mini-Con weapons—the Star Saber, Skyboom Shield, and Requiem Blaster—triggered his awakening. Shedding his lunar disguise, he transformed into his planetary robot mode, revealing his intent to consume Cybertron.

In the ensuing battle, Unicron unleashed immense destructive power, physically assaulting Cybertron and assimilating Transformers into his collective consciousness. Internal defenses, including antibodies, attacked intruders. Optimus Prime, Galvatron (formerly Megatron), and their human allies infiltrated Unicron's body to sever his control over the Mini-Con weapons. Though temporarily deactivated by a Mini-Con rebellion, Unicron revived through residual hatred from the conflict between Prime and Galvatron. Recognizing Unicron's existence depended on this cycle of hatred, Galvatron sacrificed himself by plunging into Unicron's maw, seemingly destroying the Chaos-Bringer.

Unicron's influence extended beyond Armada. In Transformers: Energon, his consciousness survived within Galvatron, who later reverted to Megatron. Megatron gathered Energon to resurrect Unicron's physical form, only to be corrupted and controlled by him. Optimus Prime, empowered by Primus, defeated Unicron again, trapping his spark within a sphere. Galvatron then carried Unicron's spark into a nascent sun to annihilate it. This act inadvertently created the "Unicron Singularity"—a destabilizing black hole threatening the universe in Transformers: Cybertron. The singularity consumed planets until Galvatron, mentally aligned with Unicron's goals, attempted to accelerate its growth and reshape reality. This plan failed, eradicating the last remnants of Unicron's influence.

Across all depictions, Unicron's core drive remained the annihilation of creation to achieve primordial nothingness. His methods relied on manipulation, psychological torment, and exploiting the Transformers' war, while his legacy persisted through enduring physical and metaphysical threats.