The counterpart to Mechanically Modified, Bio-Engineered villains are those who have been either created or enhanced through biological science, which includes cloning and/or manipulation of genes.
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- Seelkadoom the Hedgehog
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- Skyblack
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- The AI (Pokemon Maroon)
- The Deep (Every Episode of The Boys)
- The Didact (Halo 4: Genesong Cut)
- The Didact (Halo 4: Mythic Overhaul)
- The Evolved Vagineer
- The Gangs of Clever Girls (Rexyverse)
- The Hunter (Dead Space)
- The Many
- The Mastermind Vagineer
- The Powerpuff Faction
- The Powerpuff Girls (Double Rainboom)
- The Very Hungry Genetically-Modified Caterpillar
- Thebasedlander2
- Timefiend
- Titan Speakerman (The Risen One)