The story starts with the main character Leon S. Kennedy (who is also in Resident Evil 2.) He has a job to rescue U.S. president's daughter who was kidnapped and the clues of her whereabouts lead to a rural Spanish village.
Puppeteer tells story of Kutaro; a puppet who ended up in midst of an crazy adventure that nobody wouldn’t ever believe! The story starts of Little Bear who stole a Moon Goddesses Moonstone and magical scissors, Calibrus. After that he named himself as Moon Bear King and smashed the Moonstone into pieces and handed over a piece to each of his Generals so they would gain power and they all could reign the world.
The game starts with evil Dr. Quark and his boss Cabital B. (yes one is a duck-ish and other a bee-ish) plotting their evil plans and starting the huge machine that would suck all books from the world so they could write the universe again. They even manage to get Laylee's magical book scattering the pages (Pagies) all over the game world.