Neo Contra takes place during A.D. 4444 when the Earth has been transformed into a prison planet, home to criminals and political rebels (Contras). From this underworld society rises a new order called "Neo Contra". This government quickly showed its true colors, as it has other plans than bringing back normal civilization. Carrying out this new threat are four renegade contra, who are called the Four Elite. Thus, Bill Rizer is partnered with Genbei "Jaguar" Yagyu, a Samurai, and the two are sent to Earth to deal with the Neo Contra threat.