As with its predecessors, the game follows the story of a human who is mysteriously transformed into a Pokémon (determined by a personality test at the game’s start-up). Along with the starters from the previous game, five more are included as playable choices; Phanpy, Riolu, Shinx, Eevee, and Vulpix. Some, however, are only available to certain genders; Eevee, Skitty, and Vulpix are always female. Riolu, Phanpy, and Shinx are always male. However, 2 starters, Munchlax and Meowth were removed and can only be played as the partner. Many new gameplay features were incorporated into the game. There were extra dungeons added, the titular event Pokémon Shaymin featured on the box was added, and alternate forms introduced in Pokémon Platinum (except for Rotom) were included.
Explorers of Sky expands on the plot of Explorers of Time and Explorers of Darkness, as well as exploring the background of several characters. New cutscenes were added and some were changed. Five new Special Episodes are unlocked at certain points in the game which add to the overall game (such as Wigglytuff’s inspiration to become an explorer, the induction of Bidoof into the guild, the formation of Team Charm, a special mission for guild member Sunflora, and the investigation of Grovyle and Dusknoir who team up after the battle at the Hidden Land, which shows how Primal Dialga was defeated simultaneously in the present and the future and how the future continued to thrive).