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 player's goal is to stop the Phobos Battalion and to discover why it is stealing Pokémon.

How to progress through the game: 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. Players can increase their chances of finding rare Pokémon by playing wirelessly with friends. Players also can frequent the "Agent Café" and use the "Espionage Mode" to exchange "Agent Cards" with friends for a chance to catch other rare Pokémon.

Special powers/weapons/moves/features: There are four modes to play in Pokémon Trozei: two single-player, a battle mode for two players to go against each other and a mode for teaming up with a friend. The multiplayer modes use the DS wireless function. The game also has a wireless distribution mode where players can relay a playable demo version of the game – Pokémon Trozei Mini – that allows other players the opportunity to experience the game.