Five years after the events of Contra III: The Alien Wars, an elite commando unit known as the "Unified Military Special Mobile Task Force K-X", or the "Contra Hard Corps", are sent to take on the ongoing crime and illegal activities in the city following the war. An unknown hacker infiltrates the city's security system and all the unmanned robots wreak havoc. As the Hard Corps' mission goes deeper, the culprit is revealed to be Colonel Bahamut, a hero from the Alien Wars who is now a terrorist planning to overthrow the Government with the use of the Alien Cell.