The first in the series, Zoids Saga is set at a point between Chaotic Century and New Century Zero, and follows Prince 'Atory' of the Arcadia Kingdom. Atory is forced to flee his home after it is attacked by a man known only as the Emperor. It is revealed early on in the game that the Emperor is after the 'Time-Space Transmission' technology recently discovered by Arcadian scientists; wanting to use it to travel back in time and conquer Zi. Most of the game is spent travelling back and forward in time to stop the Emperor's henchmen from altering history.

The party (Atory and his three bodyguards to begin with) travel in time on several occasions in pursuit of the Emperor's four henchmen, appearing at three points during the Zoids: Chaotic Century series, twice during Zoids: Guardian Force, once during Zoids: New Century Zero, and once during the era of the Silver Liger Zero Game Boy game.

The games of the Zoids Saga series are party-based role-playing games, and involve the player character leading a team of Zoid pilots. The party moves around the overworld and through the dungeons, fighting off wild Zoids and enemy pilots as the player attempts to complete the game. The player is responsible for constructing the various Zoids available from captured technical data, assigning the pilots in his party to the Zoids, and organising them in a battle formation.

Combat is turn-based, and occurs on two opposing two by three grids, one for the player, the other for the enemy. Six of the player's Zoids (previously organized into the two by three battle formation) are deployed, and the player must use a combination of the Zoids' weapons, pilot skills, and special orders (deck commands) to defeat the enemy.