One of the features that differentiates Explorers of the Sky to its close predecessors is the inclusion of extra story elements, referred to as episodes. These episodes allow you to play through a small story as characters other than your main Pokémon and partner. This gives you more insight into the characters in the game and unanswers questions raised in the previous ones. Below are the episodes we know:

Special Episode 1: Bidoof's Wish

Set in: Past
Unlocked After: Chapter 3
Main Character: Bidoof Lv. 10
Partner Characters: Snover Lv. 22
Dungeon: Star Cave

This special episode has you play as Bidoof during his younger days. Bidoof desperately wishes to be part of the Wigglytuff Guild. However, when his attempts prove fruitless, his friend Snover gives him a map to a place called Star Cave. This cave is said to be inhabited by Jirachi, the wish-making Pokémon. Eager to have his wish fulfilled, Bidoof and Snover head to the dungeon to find Jirachi

Special Episode 2: Genius Igglybuff

Set in: Past
Unlocked After: Chapter 9
Main Character: Future Guild Master Igglybuff Lv. 17
Partner Characters: Banette Lv. 15, Skorupi Lv. 15, Armaldo Lv. 28
Dungeon: Dark Wood

The first episode has you play as Guild Master Wigglytuff back when he was an Igglybuff. Still a child living with it's two Wigglytuff parents. One day, while out playing with his friends; Smoochum, Wooper & Budew, they get confronted by a Banette and a Skorupi who wish to go to a forest dungeon to explore. While there, you end up meeting an Armaldo. This episode shows how Wigglytuff came to be interested in exploring.

Special Episode 3: Task of the Day

Set in: Present
Unlocked After: Chapter 13
Main Character: Sunflora Lv. 29
Partner Characters: None
Dungeon: Source Cave

The third special episode features Sunflora remembering how he got started. As such, you get to play through one of Sunflora's missions. Sunflora is given the task of having to hunt down a Haunter. However, Sunflora is sent in alone without any backup and thus you have a massive challenge ahead of you to get to Haunter and bring him in.

Special Episode 5: Into the Dark Future

Set in: Future
Main Character: Grovyle
Partner Characters: Dusknoir

The next episode follows on from the main storyline. After their defeat at your hands, Grovyle & Dusknoir both return to their future. Once they arrive, they are soon attacked by some Sableye, minions of Dialga, whom have been sent to dispose of Grovyle & Dusknoir for their apparent failure in their mission. Teaming up, Grovyle & Dusknoir have to go through the dungeon to find out why exactly Dialga is angry.

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