In order to be able to fly freely through the Hoenn region, the player needs to obtain the Eon Flute, which is given by Steven Stone after defeating either Primal Groudon or Primal Kyogre, depending on the version. After obtaining the Eon Flute, the player can call either Latios or Latias, depending on the version, to take the player into the sky while Mega Evolving.
While in the sky, the player has fully control of flying on the Latios or Latias. The player is able to speed up, slow down, and even to perform little tricks in the sky. The player is able to land on most locations marked on the map, as well as Mirage Spots.
- Main article: Sky Encounters