An item called the Azure Flute is present in the game's data, but can't be legitimately accessed. Hacking the flute into one's inventory triggers a battle with a level 80 Arceus in the Hall of Origin, an otherwise unused area hidden above Spear Pillar. Both the Hall of Origin and the battle with Arceus feature unique themes, which also go unused in the normal course of play.

The Azure Flute was intended as an event item to be given out to players, much like the Event Card and Oak's Letter (which allow the player to fight Darkrai and Shaymin, respectively). However, Game Freak scrapped the idea upon concluding that it would be too confusing for players. Instead, Arceus was directly given out at events.

Arceus' battle theme would later be used for the Sinjoh Ruins event in Pokémon Heart Gold & Soul Silver where players can obtain a Dialga, Palkia, or Giratina if they have an Arceus as the first Pokémon in their party. This event additionally contains code allowing it to be triggered by an Arceus from the Hall of Origin, indicating that Game Freak still considered distributing the Azure Flute this late into Generation IV. Spoiler:The Azure Flute item and its corresponding event would eventually be implemented in Pokémon Brilliant Diamond & Shining Pearl, where players can access both by importing save data from Pokémon Legends: Arceus after catching Arceus there.