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Occasionally in the Generation 4 games, instead the of the regular "Saving..." message, "Saving a lot of data..." is displayed. What causes the game to 'save a lot of data'?

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I have found another consistent way to get the game to "Save a lot of data": moving and exchanging Pokemon around in the PC. Just by moving a single Pokemon in a separate spot in the same box the save time will be extended. Even if you move the Pokemon back to where it was in the same session it will still need to take extra time to save the game. In fact, even just holding a Pokemon and placing it right back will cause this to occur, it seems something about the DS hardware made it difficult to save the changes in the PC in a short amount of time.

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From my experience of playing D/P/Pt, I have accumulated some actions that cause the game to save a lot of data...

  • defeating gym leaders/ advancing in the story
  • catching Pokemons
  • going to new routes / places
  • having your game on for a long time
  • filling a pokedex entry

Bulbapedia has some occasions on why it says 'saving a lot of data' instead of the usual 'saving'. Click here.

I will add more as I find them along the way.

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This answer contradicts the Bulbapedia page that it links to.