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The Atomon was released by an experiment involving a particle accelerator on the colonial supply base Figaro Xll by Doctor Trudo. It controlled Doctor Trudo and the base's Dronebots to feed and grow before escaping the base. Taking on the body of a Dronebot, it swore revenge on the Time Lords who waged war against them. (COMIC: The Frankenstein Particle)

Eleventh Doctor encountered the Atomon again on the planet Velgris where it was stripping the planet of its Hooji trees for its life-giving properties and threatening the native lifeforms, including the Doctor's friend Elpha. It developed a means of fusing the living matter off the Hooji tree with the metal and plastic of the Dronebots and itself. The fused Atomon teleported away but not before remarking that they would meet again. (COMIC: The Atomon Invasion)

It was not long before the Atomon set a trap for the Doctor using the kidnapped Earth President Madam Vera Fusek as bait. In a "final" confrontation the Doctor used a Vortex cannon from the TARDIS on Atomon. By bringing the atoms together (rather than as the Time Lords had done, separating them), the Doctor gave the Atomon that which it always wanted, to live as a single independent body. Reborn as a tall green humanoid, Atomon agreed to end the war with the Time Lords and was taken under the wing of the President. (COMIC: Vengeance of the Atomon)

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