Pokémon Ruby and Sapphire Versions/Internal Battery Life

Clock-based events in these games as well as are controlled by a CR1616 lithium battery in the game cartridge. When starting up a file, players may receive a notification that the internal battery has run dry, and that clock-based events will no longer occur. This does not affect the save file or progress in the game, only events that happen in real-time, such as berry growth or the Shoal Cave tides.

Even after replacing the battery, symptoms may persist in existing save files. This is because as soon as the battery runs dry, the timestamp associated with real-time events (that had been increasing steadily since the file was created) reverts to its initial value. This means that if the game was played for 5 years before the battery ran dry, it would take 5 years with a new battery for the new timestamp to catch up to the old value and for time to "progress" once more. Furlock's Forest details this issue and possible solutions.

Starting a new save file after the battery is replaced will fix the problem because all events will be triggered relative to a new timestamp.

It should be noted that the same symptoms, but lacking the notification about the internal battery, may be caused by the Berry glitch.