Mod Edit: These posts contains spoilers
The film begins with Shaymin by an oasis, as Dialga appears. It drinks from the water, before being attacked by Giratina from the Reverse World (rumored to be the "Distortion World". The angered Giratina comes through a portal, grabbing Dialga and dragging it into the Reverse World. Shaymin gets caught in a whirlwind and is sucked through the portal, too. Dialga and Giratina fight, while Shaymin tries to survive - unnoticed by the giants - the battle. A adventurous-looking man with a Shieldon watches the battles from afar, spotting Shaymin. There are also glimpses of a computer simulation observing the battle, on the ship of Zero. Zero is the film's villain, who seems to be watching Giratina with the aim of capturing it.
As the battle progresses, Shaymin absorbs a dark gas, and then does what looks like to be exploding. The explosion tears a hole in space and time, creating a portal back to the real world which pulls Shaymin through it. Dialga escapes through the portal, but it closes before Giratina can get through. Giratina keeps hitting the same spot over and over, in what the computer calls a "time loop". Dialga then flies off. Shaymin is thrown into a river, and goes out of control down a huge mountain to a small seaside town. We find Ash, Brock and Dawn in the town, with their Pokémon, enjoying Brock's cooking once more. Ash is scolded for not washing his hands before eating. As everyone is preoccupied with the Pokémon eating, a grey Shaymin starts eating "hot cakes" from the table. Piplup attacks Shaymin, causing a barbecue to be knocked over in the chaos. Shaymin absorbs the smoke and then explodes as before. Dawn saves Shaymin from being attacked by all the angry Pokémon, washing her under a tap. Its revealed that Shaymin can talk telepathically, and it talks of "that place", which irritates Ash as he can't understand. Shaymin teases Ash a lot about being stupid, but befriends Dawn.
They take Shaymin to a Pokémon Center, where Brock hits on Nurse Joy until his Croagunk punches him and drags him away (which typically happens when he hits on girls in the Diamond and Pearl saga). Shaymin says that it'll lead them to "that place", sitting on Ash's head and making him move where it wants to go as he complains. Team Rocket watch in the Pokémon Center, and decide to try to steal Shaymin. In a garden full of strange isometric and rectangular statues, the sides of some start to ripple and Giratina appears briefly. Team Rocket pick up Shaymin and run off, but are then sucked into a statue, which has become a portal to the Reverse World. Everyone except Brock is sucked through, where Ash, Dawn, Pikachu and Piplup battle Giratina while rescuing Shaymin. Running from Giratina, they bump into the man who watched the earlier battle, who introduces himself as Newton Graceland, a "genius scientist". Ash and Dawn comment on him introducing himself as a "genius scientist", and Shaymin mocks him. He leads them to a portal back to the real world, while explaining that Dialga and Palkia's battle (in the 10th film) caused a black smoke to fill the Reverse World. This infuriated Giratina, explaining its attack on Dialga in the beginning of the film. Pikachu, Piplup, Shaymin, Ash, and Dawn return to the garden, where Brock is waiting. Team Rocket appear too late, and are left behind with Newton in the Reverse World.
Back in the garden, Ash and Dawn attempt to explain about the Reverse World and Giratina, but are stopped by the appearance of Magnemites and Magnetons. Zero comes down on a hover-board, with Magnezone as his side-kick. They disable the Magnemites long enough for them to flee into the streets of the town, chased by Zero's Magnemites, Magnetons and the Magnezone. Escaping onto a train leaving town, they talk with people on the train, and Shaymin transforms into its Sky Forme when exposed to the Gracidea Flower. It is explained that Shaymin transforms when exposed to Gracidea Flowers, found at the top of the mountain, where all the Shaymin live. It is then decided to help Shaymin return home. The train is attacked by Zero's Pokémon, who are fought off by Pikachu, Piplup and Shaymin. Magnezone smashes the side of the train, but is repelled just before the train enters a tunnel, leaving all Zero's Pokémon to smash into the side of a hill.
On a boat, the group are going up a river to reach Shaymin's garden. They play around, and Shaymin teases Ash more, until Zero appears again. A portal opens in the water, sucking Shaymin and the others in, and Zero and his Pokémon follow. Ash, Dawn, and Brock battle Zero's Pokémon, and find Newton, who leads them into a cave. Giratina and Shaymin battle, until Shaymin's Sky Forme transformation wears off. It's saved by Pikachu on Staravia, who rejoin with the group. Shaymin causes another explosion by absorbing the dark gas, allowing them to escape, and Giratina and Zero follow. With everyone in the real world, a gigantic airship appears in the valley which Zero flies to with his Pokémon. Giratina changes to its normal form, and sits on the bank of the river. A gun from Zero's ship shoots Giratina, who flies up to attack the ship, but is caught in a giant trap that begins sucking Giratina's energy away.
Everyone except Brock board a hover-board and fly up to the ship, where they battle Zero's Pokémon, and Newton enters the ship to disable the computer. It is revealed in a flashback that Zero used to be Newton's pupil, studying the Reverse World, until he became obsessed with Giratina's power and decided to catch and take his power. Newton disables the computer and the trap, freeing Giratina who collapses unconscious inside the trap, but also accidentally turns off the ship's engines. The trap falls apart, dropping Giratina into the river, and the ship begins to come down. Everyone escapes on the hover-board, except Zero who stays on his ship. Just before the ship crashes, a smaller ship separates from it.
[Edited by moderator insomniac, 2/18/2009 9:05:53 AM]