The Neo Contra is the titular antagonist organization in Neo Contra. They are a military organization which arises around 4444 A.D. and takes control of Earth, which at this time had been turned into a prison planet. The group had the pretense of re-establishing organized society into the planet, but their 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 A.I. 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: