The story begins in the schoolyard, where Yū Shirogane is showing off the new Pokémon he got in Platinum Version, Shaymin Sky Forme level 50! The day before, Yū had traded his Movie Shaymin to Platinum and went to Floaroma Town to obtain the Gracidea Flower and use it on Shaymin to obtain the Sky Forme. Yū's friends are pretty impressed by this and ask if he can show off its attacks. Yū is happy to oblige, however the Shaymin refuses to obey. As Yū begins to lose his temper, his rival Shin arrives and comments on how pitiful he looks and asks Yū how many Badges he's collected. Yū replies that he only has one before Shin goes on to explain that traded Pokémon won't obey the player if they don't have enough Badges and that Yū must be a pretty pathetic player if he doesn't even know that much. Yū then loses his temper, challenging Shin to a battle so he can show off his real strength. Shin says that he'll hold off on the match for three days to give Yū a chance of maybe earning another Badge or two in the meantime. When Yū gets home, he swears to train extra hard to level up his Pokémon and have all eight Badges in time for his match with Shin. As he starts to train, he discovers the usefulness of using the types of both techniques and the Pokémon that are used against other opponents as he makes progress in the game.
On the day of the appointed duel, Yū brags to his friends about his progress before seeking out Shin for their battle. Shin tells Yū to be patient and that he hasn't forgotten as the two begin their match. A Double Battle with two Pokémon each. Shin uses Empoleon and Bronzong against Yū's Infernape and Sky Forme Shaymin. Yū goes straight on the offensive, however Shin increases Empoleon's evasion with Double Team and Bronzong's defense with Iron Defense. Shin then starts beating down on Yū's Pokémon. Yū manages to start whittling down the strength of Bronzong, Shin is smug however knowing that Bronzong's Heatproof Ability lowers the damage received from Fire-type attacks. However he forgot to take Infernape's Blaze into account, which allows Infernape to do enough damage to knock Bronzong out. However, Infernape is quickly taken down by Empoleon. Shin asks Yū if he think he can win against Empoleon with barely any damage and its evasiveness raised so he can't land any attacks. However Yū has one more trick up his sleeve, Shaymin is holding a Micle Berry which raises its accuracy in a pinch, allowing him to attack with a Leaf Storm taking Empoleon out. Shin is impressed that Yū had thought so far ahead to prepare a Micle Berry in advance. Yū replies that no one can know what will happen unless they try which is what makes battles so interesting and that this victory is now his first step to becoming the Battle King!