Months after the events of the Dark Crater, Lira, Ri, and the rest of Team Crusade are forced to halt their investigations in order to help uncover the mystery behind the ever-present disasters that remain thanks to the extensive damage done to time-space, the road ahead taking them to strangely familiar lands and unlocking secrets long kept buried.

A growlithe sets out on a quest to save her homeland, and with the help of a jolteon, scyther, and other wild pokémon, she searches for help, but all the while an enemy follows her, waiting to strike. And a much greater danger lurks, threatening them all.

[PMD—PSMD] An ancient evil is rising once again, drawing the planet towards the sun and threatening all life. Pokemon are being corrupted from the inside-out and all established order is cast to the void, slowly decaying to ash. Waking up in this unstable world, a paranoid amnesiac Snivy must discover his identity again—all while battling the darkness within himself.

Ian, once a human now turned Mudkip wakes up to find himself in a world only inhabited by Pokemon. Having no memories of his past, he meets up with a Fennekin named Patience who dreams of joining the Expedition Society. When an ancient evil awakens, turning any Pokemon in its way into stone. It is up to them to solve the mysteries of their past, and save the world from destruction.