A time meter will appear on the top of the screen, and if the player lives through the end of the level, they will be awarded bonus points for badges that represent feats accomplished.

[citation needed] One year after the events of Metal Slug 3 and 6, the world is under the threat of a mysterious and deadly cyber virus that threatens to attack and destroy any nation's military computer system.

With Tarma Roving and Eri Kasamoto unable to help out due to their own assignments in the matter, Marco Rossi and Fiolina Germi are called in to investigate the situation and are joined by two newcomers, Nadia Cassel and Trevor Spacey.

They head into battle against Amadeus' forces, hoping to destroy the cyber virus before it gets the chance to wipe out the entire world's military computer system.

The player confronts the leader of the syndicate, a man tentatively called "Doctor", who attacks with a series of powerful robots, but he is defeated and is trapped in his own devices as the base self-destructs, killing him.