Freedom City Individual Villains
- Argo the Ultimate Android (analogous to DC's Amazo or Marvel's Super-Adaptoid)
- Blackstar (analogous to DC's Sinestro)
- Conundrum (analogous to DC's Riddler)
- The Crime League (analogous to DC's Injustice Gang or Injustice Society, or Marvel's Masters of Evil)
- The Curator (analogous to DC's Brainiac or Marvel's Collector)
- Doc Otaku (analogous to DC's Control Freak or Marvel's Arcade)
- Doctor Simian (analogous to DC's Gorilla Grodd
- Doctor Sin (analogous to Dr. Zin from Johnny Quest or Marvel's Yellow Claw)
- The Factor Four (analogous to Marvel's Frightful Four)
- Fear-Master (analogous to DC's Scarecrow)
- Gigantosaur (analogous to Godzilla)
- The Green Man (analogous to Marvel's Blackheath or DC's Swamp Thing)
- Malador the Mystic (analogous to Marvel's Baron Mordo or DC's Mordru)
- Megalodon (analogous to Marvel's Lizard or DC's Man-Bat)
- Omega, Lord of the Terminus (analogous to DC's Darkseid or Marvel's Thanos)
- The Psions (analogous to Marvel's Brotherhood of Evil Mutants and Babylon 5's Psi Corps)
- Quirk (analogous to Marvel's Impossible Man or DC's Mister Mxyzptlk)
- SHADOW (a group analogous to Marvel's HYDRA)
- Star-Khan (analogous to DC's Mongul or Khan Noonien Singh of Star Trek)
- Talos (analogous to Marvel's Ultron)
- Terra King (analogous to Marvel's Mole Man)
- Toy Boy (analogous to DC's Toyman)
- X-Isle, the Living City (analogous to Marvel's Ego the Living Planet)