You play as Lucy Lightfoot in this game, a sporty and fashionable girl who possesses the skills of a secret agent. Despite her apparent girlish and clumsy looks, she's actually intelligent and imaginative in solving crisis. Lucy is secretly working under Professor P, who is the top agent of SOL (Secret Operation League). Although eccentric at times, Prof. P is a very experienced man and is also a famous inventor who is respected by many. As the name implies, SOL is a secret league of justice, and is symbolized by the Pokémon Solrock. Your goal in the game is to save Pokémon who have been taken by the evil organization the Phobos Army, which is symbolized by Lunatone.
You set out with two partners, Aipom and Manectric, and is equipped with the Trozei Beamer invented by Prof. P. After you sneek into the enemy's plane with a hang glider, you seek out the Pokéballs and scan them with x-ray from your Beamer. The Beamer will transfer 4 (or 2 and 3 later) identical Pokémon back to Prof. P at SOL each time, and that explains the game play of lining up the Pokémon icons in the game fields.
There are many generals you have to face in the Phobos Army. The green bee like one, General Buzz, who puts obstacles in your game play with throwing in rocks to interrupt your pokemon icons (which you can clear by lining them up with Ditto), or by turning all your icons into shadows The purple one with propellors under his shoes, General Avery The woman with a bubble helmet, General Aqua Leila The military green burly man, General Grock The balloon guy, Ban-Booram, who is said possess special powers