Team Rocket's memories of Mewtwo had been erased, but the Team Rocket scientists' logs have not. After uncovering the logs, they track down Mewtwo and build a Base in a Johto. Ash and company meet Mr. Giovanni for the first time.
When Pikachu is taken to the Tree of Beginnings by the playful Mew, Ash Ketchum and friends are guided to the tree by Lucario, a time-displaced Pokémon who seeks answers regarding the betrayal of his master.
An idyllic town is thrown into chaos when two powerful Pokémon, Dialga and Palkia, cross paths and battle, distorting the dimensions of time and space. The only hope comes from Darkrai, a shadowy Pokémon shunned by the townsfolk.