Marco Rossi and Tarma Roving of the Peregrine Falcon unit reunites with Eri Kasamoto and Fio Germi of SPARROWS as the quartet is ordered to investigate Morden's latest plan, being joined by two new allies named Ralf Jones and Clark Still of the Ikari Warriors.

After destroying their latest war machine in a long hillside battle, the six soldiers confront Morden and discover that he has rebuilt his alliance with the Martians.

Each character now has unique abilities: Marco's basic gun does more damage, Eri can throw bombs in multiple directions, Ralf can perform the Vulcan Punch and take two hits himself before dying, and so on.

Characters can now throw away one gun power-up's worth of ammunition, to give to the other player or simply discard altogether.

Conversely, the sliding technique from Metal Slug 5 has been removed, and players except Fio and Ralf only receive half as much ammo for special guns.

The faster the speed at which enemies are killed, the higher the power, as a meter at the bottom of the screen shows.