The Neo Contra is the titular antagonist organization from Neo Contra. They are a military organization which arises during 4444 AD and takes control of Earth, which at this time had been turned into a prison planet. The group had the pretence of re-establishing organized society into the planet, but it's true goals were to take over all colonized planets in the galaxy.
- Master Contra: The leader of Neo Contra, he is actually a large space construct whose AI was programmed with the consciousness of Bill Rizer.
- The Four Hell Warriors/Four Elite: The four commanders of Neo Contra, each is in control of a portion of the planet.
- Guerrilla Contra: A military commander who is often seen smoking a pipe.
- Plant Contra: A mutant plant/cyborg hybrid.
- Pheromone Contra: A female bionoid, she is a replica of Lucia.
- Animal Contra: A sentient, talking bull terrier.