From Pixelmon Wiki
The Azure Flute is an item that is received when completing the Arc Chalice requirements. After obtaining the Azure flute, the player can, when within range of a Timespace Altar, right click to play the flute. Once this is completed, a short animation will play and Arceus will rise from the ground. Once fully risen, it will attack the player immediately unless the player has no Pokémon that are able to battle, whereas Arceus will instead roam around the area.
Azure flute atop the Arc Chalice: