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. Allen O' Neil fights the player and is also revealed to be a machine replica. In the final stage, they find an underground facility where android doubles of Morden are being manufactured. Halfway through the game's story mode, the player is confronted by who they presume to be General Morden. 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. In their investigation, the group discovers that a rich terrorist organization known as the Amadeus Syndicate is behind the plot and and has allied with General Morden's Rebel Army. With Tarma Roving and Eri Kasamoto unable to help 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. One year after the events of Metal Slug 3 and Metal Slug 6, the world is under the threat of a mysterious but deadly cyber virus that threatens to attack and destroy any nation's military computer system. Eri and Tarma were replaced with Nadia and Trevor.

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. The time allotted is determined from the type of emblem that is picked up. A bonus scoring system was added that allows the player to be rewarded depending on how many enemies are killed in the time allotted.

Metal slug 4 game