
Although General Morden has been written off as "missing" by his followers, they have hidden themselves throughout the world, and Marco and Tarma's abilities and experience are seen as a necessity to destroy remaining rebel strongholds, one by one. Instrumental in squashing Morden's Rebellion forces, Marco and Tarma of the Peregrine Falcon Strike Force are ordered to lead the team after their earlier requests for resignation were denied.

Morden, brought back into power, was attempting another coup d'état, but government forces got wind of the plot beforehand and pre-empted the impending assault. The rebellion orchestrated by General Donald Morden to bring about a new global regime is now ancient history, and order and peace has begun to return to the world. All paths eventually lead to the same boss battle, but the player may have different equipment, and may have rescued more or fewer hostages depending on their choices. New for Metal Slug 3, however, is the branching path system in most missions, there are forking paths for the player to choose from, each with their own obstacles, and of varying length and difficulty. The gameplay mechanics are the same as previous Metal Slug games. The game was also released for the Wii as part of the Metal Slug Anthology.

The game was later ported to the Wii Virtual Console and Nintendo Switch. The music of the game was developed by Noise Factory. Being the last Metal Slug that SNK was working on until the bankruptcy, it was given a lot of features, enhancements and improvements. Metal Slug 3 is a run and gun video game for the Neo-Geo console/arcade platform created by SNK that was released in 2000 and is the sequel to Metal Slug 2.
