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
TWhen Bidoof left home and first joined Wigglytuff's Guild, it often messed things up around, and wasn't really liked by everyone. One day, while visiting the Kecleon shops, it was confronted by a Snover who gave it an old map before hurrying off. A Gligar and Bagon then appeared to be chasing Snover. The map shows a legendary dungeon known as the Wish Cave where Jirachi sleeps, and after learning about it from Chatot, Bidoof decided to go there so he may make a wish to make himself a stronger explorer.
Snover finds Bidoof at the Guild, and together they head off to the Wish Cave. However, upon reaching the end, Gligar and Bagon appeared, and Snover turned against Bidoof. It turns out that it was a trick pulled off by the three, who are a thief gang called Actors. They saw Bidoor's wealth (some $7000 dollar) when it visited the Kecleon shops, so plotted this whole thing to lure Bidoof to the Wish Cave to rob him.
Bidoof needs to fight down the three, but when he fails, everyone else from the Guild shows up to help him. Bidoof is touched that he is a cherished member of the Guild afterall. Wigglytuff help it blast open a hidden cave where Bidoof can find Jirachi, and after defeating Jirachi (Jirachi claims it is still sleeping and will automatically attack so Bidoof must defeat it to help it awaken), Bidoof makes his wish. Though given a lot of choices, at the end Bidoof will wish for new juniors to join the Guild so he could help them. The wish is fulfilled when you and your partner joins the Guild, and that's Bidoof's story.
Special Episode 2: Igglybuff the Prodigy
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 Forest
One night, Chatot secretly brings an Apple to Wigglytuff again, and saw it with the Guard Orb item (which boosts the Bug type). Chatot doesn't understand why Wigglytuff always carries this item which is of no use to himself, but Wigglytuff reveals that it is a very important item for memory keeps, and starts telling his tale.
When Wigglytuff was still an Igglybuff, it lived with its parents (both Wigglytuffs), and often hung out with other friends (Smoochum, Budew, Wooper). One day, a Skorupi and Banette appeared, and while everyone else is afraid, Igglybuff happily calls them friends. Since little, Igglybuff has always been carefree and courageous, and also possessed super strength (it once saved its father from a falling big boulder on a stormy night). Skorupi and Banette tricked Igglybuff into exploring the Dark Forest, where they find a ferocious Armaldo at the end.
Banette and Skorupi fled in fear, but Igglybuff once again stuck around and managed to befriend the stunned Armaldo. Igglybuff by accident found the correct way to read a mysterious map owned by Armaldo (he burnt it) and Armaldo discovered that Igglybuff is born to be an Explorer. The two thus visited the mysterious dungeon (called the Eastern Cave or something, I have to check again), and at the end of it, after finding the Guard Orb, an item that can boost Armaldo's stats, Igglybuff forced Armaldo to accept him as a student, and so the two began their adventure as teacher and disciple.
Time went on, and everyday, Igglybuff would go find Armaldo at the Dark Forest so they could go on new adventures. On one of their adventures, a Nidoking is seen spying on them.
One day, Smoochum and co. come to find Igglybuff at his house, but his parents told them he's out. It is only then that the Wigglytuffs realize Igglybuff visits the dangerous Dark Forest daily. The Nidoking appears, and agrees to take them to where Igglybuff is.
Igglybuff and Armaldo are exploring yet another dungeon, and at the end of it, everyone appears. Nidoking comes forward, and as a shock to Igglybuff, he reveals that Armaldo is actually a criminal hunted down by the police for a long time. Magnezone and his Magnemites appear to confirm his claim, and Igglybuff refuses to believe. It is about to burst into an outbreak when Armaldo gets arrested, but Armaldo stops him, and admits that he is indeed a criminal, which is why he was hiding at the Dark Forest.
Armaldo thanks Igglybuff for all the happy times he has given him, and says it is time it gets the punishment he deserved for his past deeds. He is certain that Igglybuff will become a great explorer, and gives him the Guard Orb as its goodbye gift. Crying, Igglybuff watches as Armaldo gets taken away. And that is why Wigglytuff still carries the Guard Orb in memory of its teacher until today.
Special Episode 3: Today's "Oh My Gosh"
Set in: Present
Unlocked After: Chapter 13
Main Character: Sunflora Lv. 29
Partner Characters: Loudred Lv. 27
Dungeon: Source Cave
The scream part actually refers to how Sunflora always 'screams' at the end of its words, and this story takes place some time after you and your partner joins the Guild. It is seen the Sunflora often gets into an argument with Loudred.
Anyway, Magnezone visit the Guild one day, and talks about a criminal Haunter. Since everyone else has work at hand, Wigglytuff bestows the mission upon Sunflora, who as an experienced explorer, couldn't find an appropriate reason to refuse or call for extra help. However, Magnezone warns that the Haunter is extremely dangerous, as it is called the Immortal Haunter.
And so Sunflora explores the Source Cave, and when it finally confronts Haunter and defeats it, it resurrects itself in a flash of light like its immortal claim. Sunflora keeps chasing it deeper and deeper into the dungeon, and Haunter soon calls upon fire types to hurt Sunflora, but Loudred appears to help her, much to her surprise. From her interaction with Loudred, Sunflora suddenly realized the truth behind Haunter's immorality. She chases it even deeper into the dungeon, and finally confirms that there are actually 3 Haunters in unison. When one faints, the other two will create a flash of light, and swap bodies, making the illusion that the Haunter is immortal, when in fact it is already another Haunter.
Together with Loudred they managed to defeat and arrest the Haunters, and Sunflora realizes the good in Loudred too.
Special Episode 4: Here Comes Team Charm
Set in: Past
Unlocked After: Chapter 16
Main Character: Lopunny Lv. 32
Partner Characters: Gardevoir Lv. 33, Medicham Lv. 31
Dungeon: Southern Jungle, Large Rock Cave & Limestone Cave
This story mainly deals with Team Charms' past adventures, and one day, they come across the Southern Jungle where a great treasure is said to be held. They were advised to stay away by a Bellossom at the entrance since past explorer teams have never been able to make it, but the three have confidence and continued their way.
Along the shoreline, they find Wigglytuff who fainted due to hunger, and they gave it an Apple, making it happy and up again. Soon, they encounter Weavile, Drapion and Arbok's team, and they had a little competition exploring the last dungeon. Before they went in, a Sentret appeared and hoped that Team Charms will help it chase away Weavile's team because they have done bad things to it in the past.
At the very end of the dungeon, they find an empty chest, and Weavile's team accused Team Charms are claiming the treasure for their own. The two teams fight, but Wigglytuff later appears to stop them, and to everyone's surprise, the chest begins to talk. Turns out, it is a Ditto in disguise, and it is revealed that both the Bellossom and Sentret were its transformations. Its intention is to keep people away from the dungeon, and they find out that the reason lies in the fact that at the deepest part of the dungeon indeed lies a great treasure, but it is a Time Gear, and Ditto must stop anyone from taking it.
Team Charms and Weavile's team agree to keep the Gear intact, and the story basically ends here.
Special Episode 5: Into the Dark Future
Set in: Future
Unlocked After: Game Completion
Main Character: Grovyle Lv. 46
Partner Characters: Dusknoir
Dungeons: Temporal Tower, Ice Mountain, Time Tunnel
Returning to the future with Dusknoir, Grovyle awakes and gets spotted by a Sableye. It begins its escape but is followed by Dusknoir. Then, at the end of the first dungeon, the Sableyes appear and to Dusknoir's surprise, they start attacking him as well. Dusknoir is surprised and is determined to find out the reason behind it. After a bit of hesitation, Grovyle agrees to join Dusknoir on its quest to find Primal Dialga since it has decided to go confront Dialga himself anyway.
And so Dusknoir and Grovyle start their adventure together, but at the Temporal Tower, they find that it is already empty. Dusknoir reveals that Primal Dialga must have realized that the past is going to be changed, and it attempting to stop it by freezing things in the Time Tunnel (the place where Celebi helped you guys travel back to the past). Primal Dialga has thus gone off to chase down Celebi, and so Grovyle and Dusknoir head off to find and protect Celebi. From the words of the Sableyes, Dialga has found another henchman to replace Dusknoir, and it is this henchman's command that Dusknoir be eradicated.
As Grovyle and Dusknoir carry on with their quest, they begin to develop some sort of untold trust and companionship. The find that Celebi is no longer is the forest where it resides, and after forcing the words out of a Sableye again, they find that it has fled to the southern island where an ice mountain is. There, the two continue exploring the dungeons, and at the end of one, Dusknoir saves Grovyle from a falling ice boulder and gets injured himself.
Grovyle tended to Dusknoir's wounds, and that night, the two had a deep conversation. Dusknoir could never understand why Grovyle would give up his life to change the past, but Grovyle tells him that a life with a short moment of glory is better than living an empty life, and although it will disappear, at least it has left his mark in the world and made it a better one.
The two resume their journey, and at the end of the Ice Mountain dungeon, they finally find Celebi, but it is being captured by Spiritomb. The ice pillars here give off sparks of electricity, and when Grovyle tries to rescue Celebi, it steps on the point where the electric signals merge, and is trapped by a powerful electric field. At this point, the Sableyes appear, and Dusknoir finally reveals that it has been lying to Grovyle all along. There was no new henchman, and he was just putting up a show with the Sableyes to trick Grovyle to where it is right now.
Dusknoir speaks of his plan to take over the body of Grovyle, so that he can use his identity, return to the past and mess things up again. But before Grovyle is about to go down, it speaks of its trust in Dusknoir, that certain moments in their adventures couldn't have been a total lie, and is sure that Dusknoir did sincerely connect with him at some point.
And indeed, the conversation Dusknoir and Grovyle had the other night changed something in Dusknoir, and it has started to question itself whether it is the right thing to blindly follow Primal Dialga's orders. At the last critical moment, Dusknoir saves Groyvle from the electric field, and Spiritomb flees.
However, Primal Dialga appears, and starts to attack Dusknoir for betraying him at the very last moment. Effects from the changed past start to take effect, and winds are starting to blow in this dark future world. Dialga leaves to head to the Time Tunnel, and Grovyle teams up with Celebi and Dusknoir on this last adventure. Finding Dialga at the Time Tunnel, they defeat him, and like what happened to your character in the past, everyone is beginning to glow and disappear.
Time begins to flow again in the future, and Primal Dialga vanishes. Dusknoir asks Grovyle if he has finally made his life shine, and Grovyle assures him that he has. With that, Dusknoir feels content and vanishes. Grovyle holds Celebi in his arms as they watch the sun rise for the first time in the future world. Celebi is astounded that the sunrise can be so breathtaking, and feels blissful that it can watch it together with Grovyle for the first and last time. With that, Celebi and Grovyle both vanish as well, and everything in the dark future starts to get restored into a time-flowing world.
Later, Grovyle finds himself, Dusknoir and Celebi still at the Time Tunnel, and is surprised that no one has to vanish. Dialga, now returned to its normal state, has also reappeared, and remarks that they are all revived because of a being on an even higher tier than itself. Joy is restored to the future world, and at the very end, Grovyle sends it wishes across time, and wants you and your partner to know that everyone still lives in the future, and that sums up the Special Episodes of this game.