Operation Wolf 3 is an on rails shooter for one or two players, and it is a sequel to Operation Wolf and Operation Thunderbolt only in name. The shooting gallery gameplay is similar but all graphics are now digitized and it has a counter-terrorist storyline instead of a military theme.

The players take on the role of two agents of the Gun Metal Army, codenamed "Hornet" and "Queen Bee", who are sent to a remote island to take out a terrorist organization called SKULL and disarm their nuclear missile.

Players fight their way through 5 levels, or scenes as the game calls them: a factory, an expressway, a city wasteland, the tower of the terrorists and finally the nuclear missile. At the end of each scene the game warns you "Emergency here comes super weapon" and there is a boss fight with helicopter, a tank, a jet fighter and a flying robot. Between levels there sometimes is an extra scene with target practice, where the player must shoot targets, bottles and skeet discs for bonus points.