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Berry glitch
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The disc for downloading a Shiny Zigzagoon, which when transferred to the game included one of the first patches for fixing the berry glitch after its official acknowledgement by Nintendo.
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Bulbapedia also has an article about Berry glitch.
PRAMA Initiative a également une page sur Berry glitch.

This article refers to a glitch in Pokémon Ruby and Sapphire when time-based events will stop. For the glitch related to when the player uses a Pomeg Berry with a relatively low amount of HP see Pomeg glitch.

The Berry glitch (Japanese: きのみ問題) is the name of a glitch where all clock-based events will freeze, including the growth of berries and the player's clock. It was officially patched in later versions of the Generation III games so it does not exist in Pokémon Emerald. The glitch causes all berries to stop growing, and occurs after the game's internal clock has been active for a currently unknown amount of time.

It is not to be confused with the game's internal battery running dry, a different problem which is explicitly mentioned while booting the game.

Fixing it

This glitch was acknowledged by Nintendo and as a result, they took action and released multiple fixes for the Berry glitch. It was probably acknowledged due to the fact that it hindered gameplay, rather than giving the player extra control over the game, and was not preventable. Below are a list of official fixes for the Berry glitch:

  1. For a limited amount of time, Nintendo allowed players to send their games in, and receive them back with the Berry glitch fixed.
  2. The Pokémon Colosseum Bonus Disc, which includes a Jirachi transferable to the handheld games and a trailer for the 6th Pokémon movie, also included the opportunity to connect the Game Boy Advance to the GameCube and have the Berry glitch fixed.
  3. In Pokémon FireRed and LeafGreen, the player could press SELECT+B at the title screen to reveal a screen titled "Berry Glitch Fix." From here, one could connect to a Pokémon Ruby or Sapphire game with a link cable and have the Berry glitch fixed.
  4. Downloading Jirachi from Pokémon Channel will fix the Berry glitch after it has been transferred to the game.
  5. When the player links an affected game to Pokémon Box, when the player saves their game in the 'Go To Adventure' mode the Berry glitch will have been automatically fixed, with the message "The Berry Program was updated".
  6. In the Japanese versions of Pokémon Ruby and Sapphire, if the player uses the e-Reader cards for the Pokémon Scoop's Winter 2004 event the cards will also fix the Berry glitch.
  7. In certain stores across the US and Japan, players could recieve a specifically marked demo disc containing a Shiny Zigzagoon and a fix to the Berry glitch.