A follow-up to the Metal Max games, Metal Saga is set in the same post-apocalyptic world as its predecessors - a world populated by bounty hunters, rangers, bandits, and mutant monsters. The player takes the role of a nameless young man, the son of a famous retired bounty hunter Eddy, who lives in a town known as Junkyard. Refusing to be a mechanic - which would lead to a quiet, yet uneventful life - the youth decides to follow in his father's footsteps: travel the world and track down fearsome outlaws for rewards.

Like its predecessors in the series - and unlike most Japanese role-playing games - Metal Saga has an open-ended world with non-linear gameplay. The fairly sparse, inconspicuous main plot develops according to the missions the player decides to take, which in their turn lead to new events and finally to different endings. The player can choose to ignore this plot and simply roam the world map, visiting various towns and other places of interest, and undertaking quests for money and fame. Some events will only be triggered if the hero has reached a certain rank as a hunter due to those activities.

Over the course of the game the protagonist may encounter several character who will join him. The active party consists of four characters and includes, besides humans, a few different types of dogs who can use mounted guns. Enemies appear randomly on the world map and in hostile areas, and combat is turn-based. Any character (except the dog) can fight either on foot or in a tank. Tanks must be acquired in specific locations or rented. They get damaged and broken, but it is possible to maintain and customize them by finding parts scattered across the world and assembling them to build new models. Based on the model of tank many different kinds of weapons, cannons, and accessories can be equipped to it, making for hundreds of different options. Tanks can even be given a custom paint job that is saved to the memory card.