Lucy Fleetfoot is a secret agent for Secret Operations League (SOL); whose mission it is to rescue stolen Pokémon from an evil organization known as the Phobos Battalion. In story mode the players goal is to stop the Phobos Battalion and to discover why it is stealing Pokémon.
Using the stylus players can line up four Pokémon puzzle pieces in a row (vertically or horizontally) to create a Trozei and add Pokémon to their Trozei List. Once a Trozei happens it can be turned into a chain reaction by lining up three in a row and then two in a row to clear those pieces from the screen. The longer a player keeps a Trozei going the higher the score. However if the pieces stack up too high and reach the top of the screen the game is over.
Another game objective is to complete the Trozei List. This list contains all Pokémon that a player has been able to Trozei. Some Pokémon are harder to Trozei than others.