In both games, the player can save to one of three slots on the save file, and can choose which memory card slot to save the game to. Breath of Fire III and Breath of Fire IV on PlayStation require one block on a memory card in order to allow the player to save. In Breath of Fire III and Breath of Fire IV for the PlayStation, and Breath of Fire V: Dragon Quarter for the PlayStation 2 console, save files are instead saved on to memory cards. These saves can be copied to other slots or even deleted manually by a player. In both games, a maximum of three save files can be stored on the Game Pak. The Game Boy Advance versions of the games save game progress on an EEPROM chip which does not require a battery to continue to store data.

These batteries will eventually run dry, after which the existing save files are deleted and it becomes impossible to save the game until the batteries are replaced. The SNES versions of the games rely on RAM constantly powered by an internal battery to save the game. In Breath of Fire and Breath of Fire II on both the Super Nintendo Entertainment System/Super Famicom and Game Boy Advance systems, the game is saved to a chip installed on the Game Pak cartridge.

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