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The Mini-Con Civil War (told almost exclusively through the toy bios of the Cybertron Mini-Con 2-packs) chronicled the fate of the Mini-Con race following the events of Armada, with particular focus on what they were all doing "off-screen" during the Cybertron story.
A group of Decepticon allied/inspired Mini-Cons made a play for power during the evacuation of Cybertron and the Mini-Con Council of Sages fought against them. A small portion of this conflict was chronicled in the Fun Publications fan club comic, but it apparently played fast and loose with the Mini-Con story (specifically the factions) established in the bios.