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A prototype is a version of the game from its development phase (typically an alpha or beta version) which was typically not meant to be released.
Contrary to common internet belief, prototypes are often not a "beta"; beta versions are when the game is mostly complete, but is lacking the finishing polish (unfixed bugs or glitches, unpolished translation, etc.). In this way, most prototypes released are alpha or pre-alpha versions, when the game is still under active development and several features are not finalized.
Prototypes usually end up on the internet by game testers, reviewers, or developers either directly by using a backup device, or indirectly by giving such test cartridges to friends where they eventually end up on eBay or simply dumped online. In some rare instances, prototypes end up being sold by pirates who mask it as the final version.
Prototypes are very interesting because they feature lots of content that was changed or removed in the final version without any trace. In many cases, they also feature debug modes of some kind.
Famous prototypes that were released include: