The Pokémon world is shown, as the camera zooms in on what looks like a graph of the inside of a computer chip, with Pokémon moving around inside and some scenes from earlier movies. In the sky, a lot of bird Pokémon and Lugia are flying around. Underwater, a lot of Water-type Pokémon are swimming around, along with Kyogre. On the mountainside, several Pokémon are relaxing. Some Seedotare hanging out of a tree in the forest, as several forest Pokémon are playing around. On a grassy field as the sun sets, several Pokémon are playing around, as a Cresselia floats by. In the big city, several Pokémon are playing on a playground. A Trainer brings out a Magmortar to battle another Trainer's Rhyperior. Magmortar hits Rhyperior with Fire Blast. Rhyperior uses Rock Smash while Magmortar uses Fire Punch, creating an explosion. In the garden, Eevee and seven of its evolutions are relaxing and Luxray is playing around.
As the sun rises, Ash is shown getting ready for a Pokémon battle. Pikachu uses Thunderbolt on Electivire. Ash and his friends arrive at their next destination, which is surrounded by mountains and a lake. Through a forest, a Shaymin is walking through as several Combee fly above. Shaymin arrives at a lake and drinks from it, as a Dialga enters from a different area of the lake. In the Reverse World,Giratina floats around, while a sphere shows Dialga from the regular world. From the regular world, a swirl in the lake shows Giratina from the Reverse World is shown floating around. From his airship,Zero observes the Legendary Pokémon. As Dialga drinks from the lake, a portal opens as a shadow of Giratina in its Altered forme grabs Dialga, changes to its Origin Forme and forces it to enter the Reverse World as Shaymin looks on and is dragged along with them. Zero and Infi observe the whole thing. As Giratina is entering back into the Reverse World, it changes back to its Origin Forme and hits the ground with Shaymin holding on to Giratina. Newton Graceland and his Shieldon run up to the two Pokémon and uses an analyzer on his eye to watch the battle between them. As he zooms in, he notices Shaymin on Dialga's tail.
Giratina and Dialga battle, as Dialga breaks away and tries to exit the portal, as Shaymin gets tossed around and lands on an edge. Dialga is able to poke its head through the portal, but Giratina again pulls it back into the Reverse World. Dialga and Giratina fight each other, as Shaymin absorbs a dark purple gas. Giratina uses Will-O-Wisp which hits Dialga as Shaymin hangs in there. Giratina uses Will-O-Wisp while Dialga dodges, and Shaymin is sent flying and uses Seed Flare to reopen the portal in fear of Giratina. Shaymin is sent flying through the portal to the regular world, lands in the lake, and helplessly goes down the stream as Zero watches through his computer screen. Dialga again tries to enter the portal and is able to get its head through, but again Giratina drags it back into the Reverse World. Dialga fires its energy on Giratina and is able to finally exit the portal to the regular world. Giratina uses a clear beam from its mouth to reopen the portal, but it is locked into a time loop by Dialga, blocking it from exiting the Reverse World when it tries to exit. Giratina tries over and over to break through, but just cannot bypass the time loop. Giratina's eyes glow red as it roars in frustration.
Dialga is free as the portal fully closes, leaving Giratina in the Reverse World. Dialga heads back to where it came from. Zero watches as Giratina continues to try to break through the barrier to exit the portal. Shaymin continues down the river and down the waterfall. With several Wingull on rocks, Ash looks out at the lake and then runs up the stairs to where Brock is making pancakes. Brock tells Ash that he must wash his hands, even though Ash pretends that he doesn't need to even with his dirty hands showing. Dawn was already washing her hands. Ash goes to wash his hands as Brock uncovers the Pokémon food to Pikachu and Piplup. Dawn brings out SwinubAmbipomBuneary, and Pachirisu. Ash brings out GliscorChimcharTurtwigStaravia, and Buizel. Brock brings out Sudowoodo,Happiny, and Croagunk. As Ash and his friends watch their Pokémon eat, Shaymin crawls on top of the table all covered in soot. Ash goes to eat the pancakes, but sees that Shaymin is eating the food already. Piplup tries to take the pancakes from it, but Shaymin keeps eating and accidentally bites down on Piplup's arm, making Piplup very upset. Shaymin shakes its body, making the soot blow everywhere and making everyone cough. Shaymin jumps on top of Pikachu, Ash's head while biting the hat, and then on top of the barbecue pit. It knocks it over as Brock was ready to use a pan if needed. Shaymin falls to the ground. The barbecue pit explodes as Shaymin absorbs the smoke from it and uses Seed Flare. The Seed Flare creates explosion sending everyone backwards and to the ground. Piplup yells at Shaymin, as the other Pokémon angrily approach it.
Dawn steps in to grab Shaymin before the Pokémon can attack, and brings it to the fountain to wash it off. Shaymin is completely cleaned as everyone looks on and it shakes off all of the water while splashing them. Shaymin reveals that it can communicate telepathically to everyone. Shaymin speaks of "that place" which no one understands what it's referring to. Shaymin turns red as it develops a fever, while Brock checks its forehead. Everyone returns their Pokémon to their Poké Balls and heads to the Pokémon Center. At the Pokémon Center, Nurse Joy and Chansey are using a lamp-like scanner to check Shaymin's condition, as a computer shows the results of the scans. Brock puts on some glasses since Nurse Joy also wears them, and shows his love to her. Croagunk uses Poison Jabto stop him from continuing and drags him away. Dawn feeds Shaymin a brown piece of food. Ash introduces himself and Pikachu, as Shaymin blows smoke in his face. Nurse Joy explains how it absorbs dirty things, and lets them out with Seed Flare. Shaymin likes to make fun of Ash for not understanding what it's talking about. Ash was not pleased with how Shaymin was being so demanding. In another room, Team Rocket listens in on the conversation about Shaymin. Shaymin jumps on top of Ash's head and makes him take it where it wants to go. Team Rocket closes the door to the other room, and decide that they want to steal Shaymin.
Ash and his friends head outside as Shaymin continues to pull Ash's head in different directions, while Ash is really upset about it. Dawn grabs Shaymin, as it blooms a few more flowers. Giratina senses that, and continues to float around the Reverse World. Shaymin leads everyone another direction through a garden by some triangle-shaped statues. The statues begin to ripple and Giratina is shown floating through on the reflection, as Shaymin senses that something is very wrong. James picks up Shaymin as Team Rocket tries to run off with it, but a portal opens from one of the triangle statues, and drags them into the Reverse World. Dawn grabs Shaymin from Team Rocket, but Dawn and Ash are also dragged through the portal and into the Reverse World. Brock looks on as the portal closes behind them. Ash and Dawn land on a stone pillar. Shaymin is very scared, as Giratina floats by, however, it notices Shaymin and begins to approach Ash and Dawn. Giratina roars as Shaymin is even more scared and thinks that Giratina wants to eat it. Pikachu uses Thunderbolt as Giratina disappears into a shadow using Shadow Force and reappears right behind them. Piplup uses BubbleBeam which hits but is not very effective.
Newton Graceland appears out of nowhere in front of Ash and Dawn, telling them to stop attacking. Giratina uses Will-O-Wisp, while Shieldon counters with Ice Beam. Newton leads them down a pathway that has no gravity, and then to a stairwell with gravity in which they climb down. Piplup, Pikachu, and Shieldon follow them, but Piplup slips, and Pikachu has to grab him before he falls. Giratina continues floating around the Reverse World. Newton claims to be a Genius Scientist, while Dawn and Ash are skeptical and Shaymin mocks him. Ash and Dawn introduce themselves to Newton. Meanwhile Brock is looking at the statue they entered and is puzzled as to what could have happened to them. Newton shows them a device that can help them find the exit portal to the real world. At a different part of the Reverse World, Team Rocket is puzzled by the way the Reverse World looks. They hide behind a wall, as Giratina floats by them. As Ash, Dawn, and Newton are walking towards the portal, they see a purple smoke. Pikachu and Piplup approach the smoke, as Piplup breaths it in he gets sick from it. Newton tells them not to breathe in the smoke as it is very dangerous. More of the purple smoke appears above them. Newton explains that during the battle between Dialga and Palkia (in The Rise of Darkrai), time and space were distorted, causing purple smoke to enter the Reverse World and fill it, making Giratina very angry, and is why Giratina attacked Dialga earlier in the movie. However, Newton reveals that Shaymin used Seed Flare, which allowed Dialga to escape.
A bubble appears around Ash and his friends that shows Brock from the real world. Ash and Dawn call to him, but Newton yells at them not to do that. Ash touches the bubble which bursts and sends Brock flying backwards to the ground. They jump across one pillar to another as Giratina floats by. Shaymin pulls Ash to jump across the pillars because Giratina is nearby. Ash almost falls, as he hits the ground hard while Giratina grabs the Shaymin. Ash's hat had hit the ground and started shaking. The real Shaymin comes out of the hat, as they realize that it used Substitute to escape and left the fake in Giratina's mouth. The fake disappears to Giratina's surprise as it floats away. They head up the pathway and reach the portal. Piplup, Pikachu, and Dawn enter the portal and exit back into the real world. Ash asks Newton if he is coming with and he says that he is staying back. Ash enters the portal into the real world, after some convincing by Newton. The portal closes before Team Rocket could enter it.
Jessie tries to jump into where the portal closed up, but almost falls as Newton saves her. Giratina continues to float around as Zero watches on the screen. Dialga continues to head back to its own world. Ash tries to explain the Reverse World to Brock, as the statue shows Giratina floating around the Reverse World. Zero notices that Dawn is holding Shaymin and heads to where Ash and his friends are at, and realizes that Giratina is seeking Shaymin's power. Shaymin continues to mock Ash about him getting frustrated with not knowing where Shaymin wants them to go. Some Magnemite andMagneton show up and surround Ash and his friends, while Zero shows up with a Magnezone. Pikachu uses Thunderbolt, while Magnezone blocks it with Mirror Shot. The explosion it created knocked out some of the Magnemite, as Ash and his friends run away into the alley. Piplup uses Whirlpool to trap the Magnemite so that they won't be able to follow them right away. They pass by a few of the townspeople on the way through the alleyway. The Magnemite, Magneton, and Magnezone follow them as Ash and his friends board a train to not be seen. The Pokémon search around for them.
Ash and his friends are relieved that they got away from the Pokémon. Shaymin pulls on Ash's ear, which hurts him. Dawn feeds Shaymin some food as Shaymin jumps into her arms. Shaymin mocks Ash some more, making him mad as it blows smoke in his face. Ash yells at Shaymin for blowing smoke in to his face. They speak to some people on the train, as Shaymin jumps into another woman's arms and feels comfortable there. Three more flowers bloom on Shaymin's body. Giratina continues to float around the Reverse World. Newton and Team Rocket are hiding from Giratina, and when the coast is clear they keep on moving. A man on the train shows everyone a basket of Gracidea flowers. The people on the train explain that Shaymin transforms when exposed to Gracidea Flowers, found at the top of the mountain, where all of the Shaymin live. Inside of the train, a ripple is showing a Giratina floating around the Reverse World and the ripple disappears again. Shaymin inhales spores from the flowers and turns into its Sky Forme. Shaymin jumps on Ash's head, and then moves around the train. Everyone decides that they will help Shaymin return to its home.
Magnezone, Magneton, and Magnemite appear near the windows of the train after having caught up with the train. The Magnemite and Magneton break through the windows of the train and prepare to attack. Shaymin goes in the middle of the Pokémon, then floats away as two Magnemite collide with each other. Shaymin uses Energy Ball which hits several of the Pokémon and some leave the train. Two Magnemite try to attack, but Shaymin dodges and they collide with each other. Pikachu uses Iron Tail to send two Magneton out of the train. Two Magnemite attack Pikachu, but he dodges and they collide with each other. Piplup uses BubbleBeam to send the Pokémon out of the window. Pikachu uses Volt Tackle and Piplup uses Whirlpool to send more Pokémon away from the train. Two Magnemite try to attack Pikachu, but Shaymin uses Energy Ball to send them away. Pikachu uses Thunderbolt to send the rest of the Magnemite and Magneton away. Everyone jumps for joy after sending all of them away. Magnezone breaks through the train window and is stuck. Piplup uses BubbleBeam, Pikachu uses Thunderbolt, and Shaymin uses Energy Ball on Magnezone to send it out of the window and hits the wall of the tunnel. The train enters the tunnel. The camera zooms out to show that the Magnezone, Magneton, and Magnemite have crashed into the wall of the tunnel.
As Wingull fly above the dock, Ash and his friends wave good-bye to the people from the train as they head off to Shaymin's home in a boat. Zero heads back to his airship to continue observing Ash and the others. The base is shown floating in the clouds. As the boat is headed towards Shaymin's home, the Pokémon play around, and the boat passes by some Spheal, Sealeo, and Walrein. Lumineon andFinneon are also seen, swimming underwater. Everyone looks on as the Water-type Pokémon jump in and out of the water. Shaymin floats all of the way to the sky and then back down to the boat. Piplup also tries to fly, but falls into the water. Piplup swims underwater, and then jumps in and out of the water. Staravia takes Pikachu into the air and flies around. Shaymin and Staravia fly together as Piplup jumps in and out of the water. Piplup tries again to fly but can't. The boat passes a rainbow and some waterfalls. Shaymin flies in and out of the waterfalls while splashing Ash. Shaymin grabs Ash and tries to bring him into the air. Shaymin and Staravia fly by some Altaria and Swablu.
Back at Zero's airship, he is watching a video of Newton in the Reverse world as he is talking with Giratina floating around. As Ash and his friends continue down the river, a ripple appears in the water and pulls everyone down into the Reverse world, including their Pokémon. Zero arrives to where they are at with his Pokémon and enters the portal as well with his Pokémon before it closes. Ash and his friends land on a rock pillar. Giratina floats by, as Shaymin uses Energy Ball on it. Shaymin uses another Energy Ball, while Giratina hits back with Shadow Force which sends Shaymin towards a wall. Pikachu uses Thunderbolt which isn't very effective on Giratina, as Shaymin is able to avoid colliding with the wall. As the sun sets, Shaymin uses Energy Ball again on Giratina, but Giratina dodges it. Shaymin uses Energy Ball, but it transforms back into its Land Forme. Shaymin falls but Staravia was able to save it. Shaymin jumps back to Ash and his friends, but lands on Ash while knocking him down. As they run away from Giratina, Shaymin is on Ash's head, reasoning that if it got eaten, Ash would get eaten as well, much to Ash's annoyance. Pikachu uses Thunderbolt, while Giratina dodges and uses Will-O-Wisp which everyone dodges.
Newton waves for them to follow him from an upside-down position. Ash and his friends follow him and are also walking upside down on the path and through a cave, as Giratina floats by. When Ash asks Shaymin where all its confidence from Sky Forme went, Shaymin simply states that it left it in the sky. Ash recalls Staravia back to its Poké Ball. Giratina continues to float around the Reverse World as Zero looks on with his Pokémon. In the cave, everyone runs into Team Rocket as they give some water to Newton. Ash asks why he is trusting them. Shaymin jumps off of Ash's head and mocks Meowth. Meowth is upset and Shaymin blows smoke in his face. A couple of Magnemite grab Shaymin and take it to Zero. Ash and his friends reach Zero, and Newton recognizes him, revealing to everyone that Zero was once his assistant, and several Magnemite trap them so they cannot move. The Magnemite circle around and send the dangerous purple gas floating towards everyone as they hold their breath to not breathe it in. The Magnemite bring Shaymin inside of the purple gas and it absorbs the gas. Giratina continues to float around the Reverse World and heads towards Shaymin. Shaymin uses Seed Flare to create a major explosion sending everyone backwards as Giratina roars. The explosion causes the portal to reopen and pull everyone up to the real world. Shaymin is now in utter fear of its most recent encounter with Giratina. However, Newton explains to it that Giratina only wanted its Seed Flare so that it could regain its ability to traverse between the real and Reverse Worlds. Giratina follows them into the real world while looking like a pink shadow. As Giratina lands, it turns into its Altered Forme. Ash notices its different appearance, to which Newton explains is likely due to gravity changes. Zero also enters the portal back into the real world along with his Pokémon. Zero's airship heads towards everyone and uses a red laser to prevent Giratina from moving. A red cage attached to the airship surrounds Giratina and traps it inside. The cage begins draining Giratina's energy. Zero jumps onto the cage as it heads back to the airship. The cage attaches to the airship while still draining Giratina's energy, as Zero jumps onto the airship.
The computer inside the airship displays Giratina and the amount of energy that was being drained. A red 3D diamond shape surrounds Giratina while draining its energy, as Ash and his friends look on. Newton reveals to everyone that he designed the airship, and wanted to absorb Giratina's power so that he could traverse between the two worlds at will. However, he cancelled the project when he realized that this would prove fatal to Giratina, and deleted all of the blueprints, which led to him and Zero leaving on rocky terms. He suspects that Zero had remembered everything he had designed. Shaymin absorbs spores from the Gracidea Flowers, it turns back into its Sky Forme. Shaymin flies around before heading towards the airship, with Newton, Ash, and Dawn following it. Brock was left behind on the ground and he is very disappointed. Zero sends his Pokémon to go after Ash and his friends. Magnezone tries to hit Shaymin with Shock Wave as Shaymin keeps dodging. Shaymin uses Energy Ball which lands a critical hit on Magnezone. Magnemite and Magneton use Thunderbolt on Ash and his friends, while they keep dodging the attacks.
Zero goes inside of his airship, as Ash and his friends approach the airship. Piplup uses BubbleBeam, while Pikachu uses Thunderbolt to try to break the cage that is surrounding Giratina. The attacks were unable to break the cage. The Magnemite and Magneton uses Thunderbolt on everyone, but Shaymin blocks the attack with Energy Ball. Magnezone uses Mirror Shot at Shaymin, while Shaymin dodges it. Magnezone tries Mirror Shot again, as it hits Shaymin and knocks it down towards the ground. Ash and his friends were able to grab Shaymin before it hit the ground. Piplup uses BubbleBeam, while Pikachu uses Thunderbolt to attack the Magnemite and Magneton so that they can get through. They land on the airship, as Piplup uses BubbleBeam and Pikachu uses Thunderbolt to hold back the Magnemite and Magneton. Shieldon uses Flash Cannon to make a hole in the entrance as they head inside. The computer screen shows that 50 percent of Giratina's energy has been drained. Chimchar uses Flamethrower, Pikachu uses Thunderbolt, and Buizel uses SonicBoom to hold off the Magnemite and Magneton. Buizel uses Water PulseAmbipom uses Swift, Piplup uses BubbleBeam, and Buneary uses Ice Beam to keep holding Magnemite and Magneton back. Shaymin uses Energy Ball to help hold them back as well. The amount of energy absorbed from Giratina reaches 74 percent by the time Newton reaches the computer.
The Pokémon continue attacking the Magnemite and Magneton, as Giratina keeps suffering inside of the cage. With a device from his backpack, Newton types on the keyboard of the computer while trying to shut down the energy draining of the machine. Zero's assistant lets her know that Newton is trying to end the energy draining. Newton finishes the typing and presses a red button to stop the energy drainage at 99 percent. The cage around Giratina disappears as it falls to the base of the cage. The engines of the airship were also shut down, as the ship heads towards the ground. The Pokémon are returned to their Poké Balls, as Ash and his friends jump on the hover car so that they do not crash to the ground with the airship. Everyone heads to check on Giratina, but it slips from the cage and falls in the water as Brock looks on. Zero sends a small ship into the water, and the airship crashes into the forest as the forest Pokémon run away from the ship. Giratina climbs out of the water and collapses to the ground, as Ash and his friends head to where Giratina collapsed.
Giratina appears to be dead, as everyone and the forest Pokémon gather around. Much to everyone's relief, Giratina takes a breath. Shaymin uses Aromatherapy to completely heal Giratina. Shaymin is exhausted, and Giratina roars after being completely healed. Shaymin hides behind Ash since it is still fearful of Giratina. Ash and Pikachu tell Giratina that they saved its life. Giratina is very thankful for everything Ash, his friends, and the Pokémon did for it. Shaymin no longer fears Giratina. In the small ship that went into the water, Zero comes out of the water and head towards everyone. Zero sends an attack towards Giratina, as Giratina counters with Will-O-Wisp. Pikachu uses Thunderbolt, Piplup uses BubbleBeam, and Shieldon uses Flash Cannon towards Zero's Ship, while only Flash Cannon makes contact with the ship. Zero uses some airwaves to reopen the portal, and uses it to enter the Reverse World.
After Zero enters the Reverse World, Team Rocket notices him, and tries to flag him down so that they can escape back to the real world. In one of the crystals of the Reverse World, Zero sees Ash and his friends. Zero destroys the crystal with Ash and his friends. The breaking of the crystal sent a shock wave that knocked everyone to the ground. Giratina uses a clear beam from its mouth to reopen the portal, and enter the Reverse World. Ash jumps into the hover car, and heads into the portal to the Reverse World as well. Zero moves through the purple smoke and continues moving through the Reverse World. Zero begins breaking the ice crystals in the Reverse World which have an effect in the real world. A glacier breaks apart and slides down towards the Ten'i Village. In the temple, aRegigigas wakes up during the commotion. Zero continues breaking ice crystals, while in the real world the glaciers keep breaking. A herd of Mamoswine notice the glaciers heading towards the village. A glacier is moving through the lake as Zero watches what's going on. Zero continues to break ice crystals, as Giratina floats by and uses Will-O-Wisp to hit the ship. Pikachu uses Thunderbolt, while Shaymin uses Energy Ball to also hit the ship. Giratina roars at the ship.
In the real world, Swinub uses Ice Shard, Buneary, BibarelBidoofAggronFroslassSentretFurret, and Abomasnow all use Ice Beam to freeze the lake to be able to stop the glacier from moving. Giratina uses Shadow Claw on the ship, but Zero pushes it against a wall. Zero attacks Giratina with his ship, while Giratina dodges and uses Will-O-Wisp to hit the ship. Ash pulls up next to Zero. Shaymin and Turtwig use Energy Ball, Pikachu uses Thunderbolt, and Chimchar uses Flamethrower on the ship. Giratina uses Will-O-Wisp on the ship. The Ship attacks and Giratina uses Will-O-Wisp, as both attacks create an explosion. Meanwhile, back in the real world, the glacier begins to break through the ice barrier that the Pokémon created. Newton recalls that it has happened before. Buneary uses Ice Beam and Swinub uses Ice Shard to try to stop the glacier, but it keeps on going. Regigigas appears on the top of the mountain, along with many Mamoswine that it has summoned. On the other side of the mountain, even more Mamoswine arrive as well.
Back in the Reverse World, Zero attacks Giratina with his ship, as Giratina hits the ground. Zero attacks with his ship again, as several ice pillars land on top of Giratina. Ash calls Giratina's name. Regigigas and all of the Mamoswine try to hold back the large glacier. It keeps moving even when they push it back. Regigigas uses Crush Grip on the glacier to try to hold it back. Meanwhile, back in the Reverse World, Zero tries to finish off Giratina with another attack, but Pikachu's Thunderbolt collides with it and creates an explosion. Pikachu uses Thunderbolt, Shaymin uses Energy Ball, and Chimchar uses Flamethrower to attack the ship. Zero hits Ash and his Pokémon with part of the ship, and knocks them off of the hover car and onto his ship. Zero uses gripping claws to grab Turtwig and Chimchar, as Ash and Pikachu run away from them. Ash is cornered, as the claws come towards him. Pikachu uses Thunderbolt and Shaymin uses Energy Ball to destroy them. Ash recalls Turtwig and Chimchar to their Poké Balls to get them out of the grip of the claws. Zero shows himself to Ash, as Pikachu gets ready to use Thunderbolt on him. Giratina is still stuck underneath the ice pillars, as the purple smoke floats by with Team Rocket looking on. Zero closes his ship door, as he takes the ship into the purple smoke. Ash and Pikachu try to not breathe in the smoke, as Shaymin steps in to absorb the smoke.
Back in the real world, Regigigas keeps trying to hold back and stop the glacier with Crush Grip. In the Reverse World, enough of the purple smoke has cleared, so that Ash and Pikachu are able to breathe again. The claws go after Pikachu and Shaymin again, as Pikachu uses Thunderbolt to send them back. Giratina grabs part of the ship and tries to bring it to the ground, but Zero uses a beam to attack Giratina. Shaymin uses Seed Flare to reopen the portal so that they can reenter the real world. Zero tries to attack Shaymin with his ship, but Giratina holds onto the ship. The portal opens as Team Rocket holds on to the ground, and Ash holds onto the ship so that they do not fall. Giratina uses Will-O-Wisp on the ship as it goes through the portal, and crashes onto the ice in the real world. Mamoswine and Buneary use Ice Beam, and Swinub uses Ice Shard to freeze the ship in place. The whole ship shuts down. Shaymin goes through the portal into the real world, and crashes down onto the ice. Shaymin flies into the air, turns into its Land Forme, and falls into Dawn's arms. The portal closes, as Team Rocket, Ash, and Giratina are still trapped inside of the Reverse World.
Ash rides on Giratina, as they float around the Reverse World. Giratina uses its powers to restore the ice pillars back to the way they were. In the real world, the glacier finally stops in its place. Giratina opens up a portal to the real world, as Giratina and Ash come through into the real world and Ash waves to everyone. Shaymin turns back to its Land Forme after coming into contact with the ice. Giratina comes down onto the ice, as Ash jumps off to be with his friends. Giratina roars and flies high into the sky, as Newton uses a gadget of his to analyze it. Later on, many more Shaymin appear in the field of flowers. As the sun rises, the Gracidea Flowers bloom as the other Shaymin turn into their Sky Forme and fly into the sky. Shaymin cries as it enters the field of Gracidea Flowers and turns into its Sky Forme, as it flies high into the sky. The flower petals go flying as the Shaymin circle around in the sky. The Shaymin fly over everyone's heads and head far off into the distance. Ash and Dawn tear up as they say their final good-byes to Shaymin.
During the credits, pictures of Ash and his friends sending Gracidea Flowers and heading off in a boat are presented. Regigigas was shown looking over the ice-covered area while some Mamoswine ran around. Ash and his friends made it onto the dock, as Ash catches up to Pikachu while he was running. Zero's ship is unfrozen as Newton helps him out of the ship, and Officer Jenny arrests Zero. The delivery man is shown delivering the Gracidea Flower gift baskets to Delia, Johanna, and Flint on behalf of Ash, Dawn, and Brock. Magnemite, Magneton, and Magnezone are seen floating around the tunnel, and the Aron, Lairon, and Aggron are feasting on the remains of Zero's airship. Team Rocket is shown to be back in the real world, as they walk by the temple and are hit by Regigigas ropes which sends them blasting off. Shaymin is shown sleeping prior to the sun rising, and then it turns into its Sky Forme as soon as the sun rises. Ash and his friends head off to their next destination in the Sinnohregion.


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