Distortion: Giratina, wounded from fighting Dialga in the Distortion Realm during the struggle of Shaymin, fled to the Shinjoh Ruins. Opening a portal to pass through, Giratina lost it's power when halfway through the portal, thus locking it between the Johto region and the Distortion World. Due to it's situation, Distortion pockets began to appear throughout the Johto region, causing some routes to be unable to pass. The three legendary dogs noticed this disturbance and began to investigate, feeling a duty to protect the Johto region.

Pokemon World Tournament: The age old question in the universe of Pokemon: Who will be the Pokemon master? People finally wanted an answer to this age old question. One organization funded the building of a massive building, built to hold the largest tournament known to trainers. Flyers were spread through the world, trainers from each region scrambling to join the World Tournament. Who will be the Pokemon Master? Only the World Tournament will decide.

Generations: The most known academy in the world has brought so many students to apply, though only a few get accepted. Choosing a path, one can follow that path through to the end, becoming the best they can be with the classes that are offered that both test their knowledge and hands on skills.

Project Gijinka: Having spent several years on a way to make humans live longer, Cornelius was obsessed with combining the DNA of Pokemon with humans. He not only lost his previous job, but he also lost the love of his life. With nothing left, he strove to finish his project. And he succeeded. One night, he successfully combined his DNA with a Darkrai's, having obtained a sample from the previous night when he ran across the wounded dark type. Randomly selecting subjects to undergo tests, he chose a secluded place in the middle of a vast body of water and set up the living quarters and laboratory for his experiment. Now all that was left to do was observe and study.