The year is 4444. Earth has become a prison planet home to criminals, terrorists, and many other political rebels. Bill Rizer has been assigned to a new partner, an alien samurai named Genbei Yagyu, or Jaguar. Their mission is to deal with the Neo Contra threat, and defeat the Elite Four of the Neo Contra organization, Guerrilla Contra, a robot tank pilot and pipe-smoking military commander, Plant Contra, a plant cyborg hybrid, Pheromone Contra, the only female member of Neo Contra who has connections to Bill Rizer from the past, and Animal Contra, a talking bull terrier who serves as a captain of an aircraft carrier, before dealing with the shadowy leader of Neo Contra, Master Contra, who also has ties to Bill Rizer.