A mountain with a Poké Ball pictured around it, and surrounded by clouds is shown, as Mew floats past Mewtwo. Mewtwo uses Shadow Ball to hit a Lugia, creating an explosion. Lugia flies up to the sky as ZapdosMoltres, and Articuno fly by. A group of Unown break apart, showing an Entei on a rock, as Articuno flies by. Entei uses Fire Spin, which circles around a Celebi. Celebi uses an unidentified attack to send the attack away. Celebi passes by a Suicune as Suicune jumps down off of a tall rock. Latias and Latios fly by the flat mountain with a Poké Ball pictured on it. The flat mountain explodes, as a Groudon comes out from underneath it. A Jirachi floats above the Groudon and floats to the sky as a shine of lines in the sky form. A Deoxys and Rayquaza come down from the sky, as Rayquaza uses Hyper Beam on a rock. Out of the rock, a Lucario jumps out and on to another rock. Lucario looks down, as RegirockRegice, and Registeel use Hyper Beam at more tall rock pillars. Big waves appear, as a Kyogre jumps out of the water and dives back down. As Kyogre is swimming underwater, a Manaphy is also swimming underwater. The camera zooms out to show the Pokémon world as it looks from space. Mew and Ho-Oh fly above the Pokémon world in space, as Ho-Oh shines in a golden aura.
Ash is shown looking out into the world. As he's walking, scenes from the first movie with Mewtwosecond movie with the Legendary birds and Lugiathird movie with Entei and Unownfourth movie withCelebi and Suicunefifth movie with Latias and Latiossixth movie with Jirachi and Groudonseventh movie with Deoxys and Rayquazaeighth movie with Lucario, the Legendary titans, and Mew, and the ninth movie with Manaphy and Kyogre were shown. Ash and his friends are shown on a cliff playing with their Pokémon by the ocean. Across the sky and into another dimension, an explosion sends a group of Unown backwards, as a Palkia in a pink aura, and Dialga in a blue aura are facing each other.
Inside a house, Tonio is reading a book of his on time and space. His computer shows that there is a disturbance going on with time and space, as it causes the house to shake, and the hourglass to shake and move. The hourglass falls off of the desk. In the other dimension as lightning continues to strike, Palkia and Dialga charge towards each other. Palkia hits Dialga with Aura Sphere and Dialga strikes back with Hyper Beam. Palkia blocks the attack with Protect. Dialga uses Draco Meteor and Palkia uses Aura Sphere again. Palkia's pink gem on its arm glows while it uses Spacial Rend as Dialga uses Protect to block it. Dialga's blue gem on its chest glows, its tail expands as it uses Roar of Time to hit Palkia. An explosion occurs, sending the Unown backwards. As the smoke clears, Palkia's arm gem is shown to be cracked and the light goes out. Palkia roars as Dialga uses Hyper Beam, but it dodges the attack. Palkia uses Aura Sphere, as Dialga dodges and uses Hyper Beam. Another explosion occurs, as the hourglass finally hits the floor of the house and breaks.
Ash and his friends walk down the pathway as they head to Alamos Town. They come to a large lake with mountains surrounding it, and realize that they are lost. A hot-air balloon with a girl named Aliceand her Chimchar. As a few Pelipper fly across the lake, Alice, Ash, and his friends ride the hot-air balloon towards Alamos Town. Brock tries to check his schedule for an opening to go out on a date with her, but can't find an open slot. Croagunk pops out of his Poké Ball and uses Poison Jab on Brock to stop him from going after her. Chimchar uses Flamethrower to make the hot-air balloon go higher to go to Alamos Town. Alice takes a leaf whistle and makes some music that brings Pelipper, Pidgey, and Pidgeotto to them. Pikachu goes up to meet Alice's Chimchar. Some Drifloon and Drifblim pass by the balloon. Following behind the hot-air balloon, Team Rocket is in a Carnivine hot-air balloon. A Drifloon runs into Jessie and she knocks it away. She tries to capture Drifloon with a net but keeps failing, as it angers the balloon Pokémon. The balloon Pokémon use Ominous Wind to send Team Rocket blasting off.
Ash and his friends finally arrive in Alamos Town. A disturbance in the air causes the hot-air balloon to go out of control, as Tonio's computer warns about a disturbance in time and space. After everything calms down, the hot-air balloon heads into town. On the street, a Bronzor and Gible use Tackle on each other. Gible attacks, and Bronzor uses Protect, causing an explosion as Beautifly flies overhead. Ash and his friends check out the sites, and stop by a cotton candy stand. Everyone eats the cotton candy and Pikachu and Chimchar do as well. Ash runs into Torterra and his friends run into three Pokémon Trainers.
Pikachu uses Thunderbolt on Torterra, but it has no effect since Torterra is part Ground-type. Torterra uses Seed Bomb as Pikachu dodges and uses Iron Tail to knock Torterra out. Piplup and Empoleonhave a pride contest, taking a deep breath and buffing themselves up, but Piplup falls down and rolls backwards. Croagunk uses Poison Jab, as Infernape counters with Focus Punch. Infernape uses Flamethrower which almost hits Brock after Croagunk dodges. Croagunk and Infernape try to punch each other. An East Sea Shellos climbs up a pole, and Alice and Chimchar observe the battles. Piplup uses Whirlpool and Empoleon uses Ice Beam to freeze it and break it apart. Piplup uses Peck and Empoleon uses Drill Peck at each other. Piplup uses BubbleBeam as Empoleon charges at him. Piplup spins and uses Whirlpool, as it collides with Empoleon.
Everyone heads down the stairs and stops by a fountain. A few Finneon and Lumineon are swimming in the fountain. Yanma, Yanmega, and Combee fly over the fountain. In the garden, ShinxLuxio,AzurillAzumarill, and Marill watch from behind the bushes. They greet Lisa, Ash, and his friends once they pass by. Ash brings out StaraviaAipom, and TurtwigDawn brings out BuizelPachirisu, andBunearyBrock brings out Sudowoodo, Croagunk, and Happiny. Ash and his friends plus the Pokémon walk passed a fountain, as Buizel and Piplup swim in it instead of running passed it. They run down a flower pathway, and run into a Plant Cloak Wormadam. Several Wormadam and plant cloak Burmy drop down from the ceiling to greet them. The Pokémon run across the pathway on top of the water. Happiny falls into the water, but Quagsire catches her. Quagsire swims in the water, with several Wooper following it. The Pokémon run down some steps. Ash and his friends go to the end of the Flower pathway, and check out the view of the lake and the mountains.
At the Pokémon park, Aipom, Pachirisu, and Piplup slide down a slide. A few Wooper and Happiny run around some small logs as Quagsire looks on. Azurill, Marill, Buneary, Chimchar, and Pikachu play on the teeter-totter as Azumarill helps them go up and down on it. Happiny uses its strength to carry Quagsire around, and Wooper run around as well. Two Budew, and a Cherubi jump down from a tree branch and land on top of a swing set bar where Staravia is on top of. Sudowoodo is and Croagunk are swinging on the swings with a few Kricketot with them, as a Yanma flies by. Turtwig and Shinx also slide down the slide, as Luxio watches them. Piplup jumps over a branch on the ground and goes to get Pecha from a tree. Pachirisu grabs one, Aipom grabs one, and Shinx grabs the last one as Piplup and Shinx fight over it. They roll down the hill and land on one side of the teeter totter, which sends Azurill and Marill flying. Azumarill and Buizel catch them before they hit the ground, but Pachirisu usesDischarge as Piplup and Shinx run into everyone. Shinx falls on Buneary, as she uses Ice Beam on it. Shinx hits Azumarill to break free of the ice. Luxio uses Thunderbolt, as all of the Pokémon are mad each other. Ash and his friends see what is going on, run down the steps to try to break up the fighting, and Alice uses the leaf whistle from earlier to make music, for them to all calm down. All of the Pokémon calm down, and three Pidgey come to the park.
Aipom hands the Pecha Berry to Shinx and Piplup to have them share it, as they break it in half so they can both eat it. Ash and his friends go back up the stairs to hear more of the music. A Galladejumps through some trees and in front of everyone. He tells them that there is trouble to take care of. Everyone returns to their Poké Balls and they head off to where the problem is. They find some broken pillars that look like they were chewed to fall down. Baron Alberto comes out of an opening, greets them, and discusses the broken pillars. He believes that Darkrai was responsible for it. Team Rocket watches from a distance with binoculars. He brings out his Lickilicky and has it use Hyper Beam into some bushes. Tonio was hit with the attack, and comes stumbling out with his computer, and a Drifblim. Baron Alberto thought that it was a Darkrai hiding in the bushes. As the sun shines brightly, the Cherrim had become their bright sunlight form and were dancing in the sunlight. Tonio shows Alice the disturbance readings on his computer, and then studies the broken pillars very carefully. A piece breaks off from the pillars and hits Tonio in the head. Baron Alberto shows his love to Alice, but she rejects him. That is a relief for both Brock and Tonio, who appear to like her. Dawn steps in and pushes Alberto away from her. Tonio tries to grab her, but she runs away to Tonio for protection. Tonio recalls when he would hold Alice in his arms after saving her, and that she would hug him while thanking him.
Meanwhile back in the other dimension, Palkia and Dialga continue to fight each other. They both use Hyper Beam at each other creating an explosion, scaring the Unown again and sending them backwards. The Pokémon sense that something is wrong, as the area glows a bit green, and the computer screen is showing a major disturbance in time and space. A shrine breaks and falls down, as a dark shadow moves around the trees making the sunlight dim and the Cherrim return to their non-bloomed form. The shadow comes out of the ground with glowing green eyes, and reveals itself to be Darkrai. Darkrai yells at everyone to go away. Team Rocket looks at Darkrai through their binoculars and decide they want to capture it. Lickilicky uses Hyper Beam which doesn't connect, as Darkrai moves in front of them. Darkrai uses Dark Void which hits Ash and puts him to sleep. Ash lands hard on the ground in the park, and walks around. A large scary shadow with green glowing eyes appears in front of him, as a pink creature of some sort attacks him. Darkrai appears, as Ash tries to throw a Poké Ball it disappears instead of a Pokémon coming out of it. Darkrai drops down below the ground while creating a crater on the ground. The crater tries to pull Pikachu and Ash in, as Ash holds on to Pikachu. They fall into the hold and keep falling in a dark area. Pikachu uses Thunderbolt in the real world to finally wake them up from their nightmare.
Ash and Pikachu wake up in the Pokémon Center where Nurse JoyChansey, and his friends are there to make sure that he is okay. Tonio looks at the woodwork on the floor, says to everyone that time and space are going to be destroyed, and heads back to his house, while everyone is puzzled. He looks through Godey's diary and notices a picture of him and Alice on a bench. A young Alice runs outside and sees some Budew around a sleeping Roserade and a sleeping Kirlia who are both having nightmares. She sees a Luxray attacking a Darkrai with Hyper Beam, but is put to sleep by Dark Void. She runs to Luxray and sees the Darkrai collapse by a tree. She goes approaches it as Godey looks on. Alice plays her leaf whistle so that all of the Pokémon can recover. Tonio sees a picture of a very important tower which holds a large musical instrument.
Meanwhile, at Baron Alberto's house, Team Rocket goes to him disguised as TV crew people so that they can help him go after Darkrai. The next day in the street area, Dawn is buying some jewelry, as Pikachu and Chimchar are playing around. As Ash and his friends walk through the street area, Ash remembers his terrible nightmare. They see a large building that looks exactly like the one Tonio was looking at earlier. Once inside, they see a large open space in the building, with colorful designs on the ground, and seats around the building. They see a big stone monument with a lot of Pokémon carved in it. Above their heads, they see several moving gears hanging from the ceiling. They enter Tonio's office, and see him lying on the ground as Alice rushes to him. It ends up that he was just lying down to take a nap. Tonio hands Alice the photograph that he was looking at earlier with her and Godey on a bench. Alice explains the picture to them. On the back of the picture is the music score of the song Oración that she was playing on her leaf whistle before. The Pokémon find some old music disks, as Piplup sends one in the air and Pikachu catches it before it breaks. Pikachu loses his balance, and the disk goes flying again and Ash has to catch it. Ash places the disk back where it belongs, and notices open spaces for other disks. Tonio tells them about the music playing machine, and they decide to go and see it.
They climb up the stairwell to go and see it, but are having trouble getting up the stairs because there are so many. At the top, the ceiling is see-through and very colorful. Several Pidgey fly away as an opening near the stairwell shows Ash continuing up the stairs. Ash is getting very exhausted as he is going further and further up the stairs. He looks out of the windows and sees his friends riding in a hot-air balloon to the top. They decide to let him continue on foot for exercise even though he wants to join them in the hot-air balloon. Once they reach the top, they see the music play, as several Pidgey and Rattata are sitting on it. After awhile, Ash finally reaches the top while being completely exhausted. Tonio uses a lever to move the disk holder so that they can take one of the disks out and put another in. Alice pulls down on the lever, which starts the music machine as it begins playing music from the disk. The whole town hears it as people start dancing in the streets. Pidgey pull up the balloon, Chimchar uses Flamethrower to get the hot-air balloon moving, and they head back down to the ground.
Once they reach the ground, the Trainers that they battled before ask for another Pokémon battle. Brock brings out Sudowoodo, Dawn brings out Buizel on one side, while Maury brings out Torterra, andAllegra brings out Infernape for a Double Battle. On the other side of the street, Ash uses Pikachu, and Kai brings out Empoleon. Pikachu moves in to attack. Meanwhile in the Unown dimension, Palkia and Dialga are still fighting, with Unown nearby. Dialga uses Hyper beam to hit Palkia. Dialga uses Roar of Time, as Tonio's computer starts indicating that there is a disturbance with time and space again. Palkia tries to get away from Dialga and enters through a portal to try to escape it. The portal opens up in the regular dimension, causing a pink light to shine, and strong winds to blow through the town. The computer is showing that the disturbance is even greater than before. The portal closes while the wins and light stop showing. In the Unown dimension, Dialga roars.
As Ash and his friends look at the building, Darkrai comes up from the ground behind them. Ash wants to battle it, but Alberto decides to go after it instead and brings out his Lickilicky to attack. Team Rocket videos Alberto and his battle as they comment on it. Lickilicky uses Gyro Ball, but Darkrai dodges and uses Shock Wave which stops Lickilicky's Gyro Ball. Lickilicky uses Hyper Beam, while Darkrai dodges and uses several Dark Void orbs which hit many of the Pokémon on the street. Buizel uses Water Gun while Darkrai dodges and hits it with Dark Void. More Pokémon are hit by Dark Void and fall asleep. Ash chases after Darkrai as Pikachu uses Thunderbolt, but Darkrai disappears back into the ground. Murkrow fly over the roof of a building, as Ash passes by and tries to locate where Darkrai went. Down a certain alleyway, the surrounding area turns to shadows, as Ash slowly keeps moving. Ash sees what looks like a Bibarel that is in a dream while surrounded by a pink aura floating through in and out of walls. Ash sees a shadow of Darkrai go across walls and back down the street. Pikachu uses Thunderbolt on the shadow, as Darkrai reappears from under the ground. Pikachu uses Volt Tackle while Darkrai uses Double Team to dodge. Pikachu tries to attack all of the fake and real Darkrai with Volt Tackle, but cannot connect.
Alberto and Team Rocket arrive to confront Darkrai. Lickilicky uses Hyper Beam, while Darkrai dodges and uses Dark Void to put it to sleep. Alberto checks on Lickilicky, as Darkrai disappears underground again and Ash tries to go after it. The Bibarel from before again goes in and out of walls, which scares Team Rocket. Lickilicky and Alberto turn pink, as Alberto turns completely into a Lickilicky, which shocks everyone. Ash has Pikachu use Thunderbolt to make sure Ash is really still awake, and he was. Jessie holds up a mirror to Alberto to show him what he turned into, as he screams after seeing that he is now a Lickilicky. The sky starts to look cloudy and black. At the Pokémon Center, Nurse Joy, Dawn, and Brock look after all of the Pokémon that were affected by Dark Void. Buizel, Bronzor, andTropius all show their spirit selves floating around inside. Alice and Tonio bring two more Pokémon affected by the attack, a Pidgey and Murkrow as they place them on the mats. Ash and Alberto run into the Pokémon Center, as everyone is in disbelief of seeing Alberto as a Lickilicky. No one really wanted to believe that he really was Alberto and not a real Lickilicky. Team Rocket drags the real Lickilicky in, as Tonio looks at his computer and studies how the Pokémon are able to have their spirits leave their bodies while they are stuck in a nightmare. The three Pokémon Trainers from before, run in and tell them about the fog surrounding the town outside.
Everyone goes outside and sees the thick fog covering the whole town. Allegra brings out her Honchkrow and has it use Defog to try to get rid of the fog, but the attack doesn't get rid of it. Ash and Pikachu try to run through the fog to leave the town, but end up back on the other side of the street behind everyone instead of leaving the town. Alberto is still convinced that Darkrai is responsible for everything that is going on, and tries to convince the other people of that as Team Rocket records and comments on what he is saying. Jessie says something she shouldn't, and Alberto uses Lick on her. The rest of the townspeople decide to follow Alberto to confront Darkrai, along with the three Trainers that Ash and his friends battled earlier. Alice and Tonio tell Ash and friends that there is likely something else going on that is responsible for everything that is happening. Tonio tells them that when he was a young boy, he was walking down the road, and talks to young Alice that is on top of the cliff. The rocks break from underneath her, as she falls off the cliff and closes her eyes. Tonio runs after her, as Darkrai appears and saves her from crashing to the ground. Darkrai places her gently on the ground and disappears, as Tonio goes to check on her to make sure that she is okay. She wakes up and hugs him, thinking that he was the one who saved her and not Darkrai.
Tonio explains the whole truth to Alice, much to her surprise. After hearing Tonio's story, Ash and his friends are convinced that Darkrai couldn't be responsible for everything that has happened. Tonio explains that the distortion caused from the spiritual images of the sleeping Pokémon was caused by an multidimensional disturbance from when Palkia entered their realm. As Team Rocket films everyone, they head towards Darkrai to confront it. Jessie says something she shouldn't have again, and Alberto uses Lick on her once again, grossing her out. Maury points Darkrai out to everyone, as Darkrai is standing on the top of a building. Drifblim flies over the building that Tonio is in, and records everything that is going on as the computer shows Tonio everything. Tonio studies the broken pillars from before on his computer, the outside of the building that he is in, and the rest of the town. He sees a burst of wind break out from the portal above the towers, as the computer shows an increase in the time and space disturbance. The winds stop, and he plays back the recording of it while zooming in to find the silhouette of Palkia stuck in between the two dimensions.
Infernape uses Flamethrower at Darkrai, as CrobatMasquerain, and Ledian are flying around nearby. Infernape uses Focus Punch while Darkrai dodges it and lands safely on the ground. Empoleon uses Ice Beam to freeze Darkrai, but Darkrai breaks free easily of it. Torterra, Infernape, Empoleon, Masquerain, Ledian, Crobat, and Tangrowth surround Darkrai along with their Trainers. Torterra uses Bullet Seed, Infernape and Stunky use Flamethrower, Rhydon uses Hyper Beam, Tangrowth uses Shock Wave to hit Darkrai, as Team Rocket reports and records everything. Darkrai survives, and uses Dark Pulse on all of the Pokémon that attacked it. Darkrai then uses Dark Void to put all of the attacking Pokémon to sleep, as Team Rocket records and reports what happens. Jessie was impressed by Darkrai and then proceeds to yell at it. Alberto decides that he should give battling a shot, and tries Gyro Ball which Darkrai dodges. Alberto grabs Darkrai with Wrap, while Darkrai swings Alberto's tongue, knocking him into Team Rocket and blasting them off into a tree.
Back at the Pokémon Center, Tonio uses his computer to zoom in on where he saw Palkia above the two towers, and shows them to Ash and his friends. He enhances the quality of the image to make it very clear that it is indeed a Palkia. The spirits of the sleeping Pokémon continue to float around the room. Girafarig is now one of the Pokémon spirits floating around as well. The winds from the portal appear again, while Darkrai tries to use Dark Void towards it, as everyone watches everything on the computer screen. Ash remembers that during the nightmare he had, Darkrai was trying to warn him about Palkia and Dialga. Palkia from the portal sends a circular wave through the town as Ash and his friends run to the building with the towers. Darkrai attempts to go after Palkia in the middle of the towers, but a barrier sends it backwards and Darkrai hits the ground hard. Palkia keeps sending circular waves through the town. Darkrai reappears from the ground and uses Dark Pulse which penetrates the barrier, hitting Palkia and waking it fully up from the portal. Palkia turns the town into the Unown dimension, as white and red lightning hit the ground, the whole sky and clouds turn completely black, and the clouds move in a very strange fashion across the sky. The Pokémon at the Pokémon Center all wake up from their nightmares, as their spirits that were floating fade away. After Lickilicky wakes up, Alberto turns pink and becomes human again. Alberto looks in the mirror to make sure that he is human again and yells in joy. Alberto looks up in shock, as lightning strikes down and the sky looks black. The sky surrounding the whole town is completely black.
Sudowoodo and Buizel run to hug Dawn and Brock after they wake up, and Lickilicky comes with them. Tonio's computer shows that the spirits are no longer floating around and have disappeared. Palkia lands on the ground in front of the tower and cries out in pain with its left arm injury. Darkrai hits Palkia with Dark Pulse. Darkrai uses Shock Wave, while Palkia uses Protect to protect itself. Palkia chases after Darkrai around the towers. Palkia uses Aura Sphere, while Darkrai counters with Shock Wave. From inside the portal, Dialga hits Darkrai and Palkia with Draco Meteor. Dialga comes fully out of the portal and into town. Dialga and Palkia collide and hit the ground hard. As they are fighting each other, much of the town begins to disappear completely. Team Rocket tries to run away, as Palkia and Dialga fly over them. Dialga uses Hyper Beam which hits Palkia, and it hits the ground hard as Dialga lands on the ground.
Dialga roars as blue colored waves spread across the town, shaking the buildings and affecting everyone. Dialga uses Hyper Beam, while Palkia uses Aura Sphere, which creates an explosion that shakes the ground. Palkia and Dialga continue attacking each other with Hyper Beam and Aura Sphere, as one Aura Sphere hits Darkrai at the building with the two towers. Dialga and Palkia face each other, as lightning continues to strike down. Palkia uses Spacial Rend, While Dialga uses Roar of Time which collide and create an explosion that sends strong shock waves through the town. They affect everyone, including Darkrai. Much of the town continues to disappear, as Dialga continues to use Hyper Beam, which hits the ground around some Combee as well. Dialga's Hyper Beam destroys more of the town as well. Alice runs up to Dialga and Palkia and yells for them to stop fighting. They fall towards her, but Darkrai steps in and uses Dark Pulse to send them backwards and away from Alice. Darkrai goes in between the two, as Dialga uses Hyper Beam, and Palkia uses Aura Sphere. Darkrai tries to hit them with Dark Void, but they both use Protect to avoid being hit by the attack. They use Hyper Beam and Aura Sphere to hit Darkrai while sending it through the trees and to the ground hard.
Everyone runs towards Darkrai, as Palkia and Dialga continue fighting each other. As the Pokémon from earlier in the movie look on, Alice approaches Darkrai. Alice puts her hand on Darkrai, as it thinks that she is Alicia. Alice tells it that she is her granddaughter Alice instead. Ash and Dawn apologize for not believing and understanding Darkrai earlier, as Darkrai goes back underground. Darkrai heads back to Palkia and Dialga. Dialga uses Draco Meteor to hit Palkia, while Darkrai uses Dark Pulse to redirect the attack to the trees. Everyone looks on as the buildings of the town continue to disappear as the computer warns them about it. The townspeople run away, as Palkia and Dialga continue fighting each other, and the town continues to disappear. The computer shows that if it continues, that the whole town will eventually disappear. Team Rocket is running away from the disappearing buildings, and are barely avoiding disappearing themselves. Tonio remembers reading Godey's diary about the music machine and the Oración song the diary talks about. They look at the back of the picture and Tonio suggests that they should play it with the music machine, and that it can stop the chaos and destruction that is going on by calming Palkia and Dialga down.
Alice heads inside of the building with the two towers, and remembers listening to her grandmother play music on the leaf whistle. After playing the leaf whistle, her grandmother explained what else the leaf whistle has the power to do. She realizes that the song she had been playing recently on the leaf whistle is the same song that her grandmother played when she was a young girl. She looks at the music machine as it looks like it has a person playing the leaf whistle on it. She notices the disk holder where the disk is, that the music machine must play to work. Ash and his friends come and turn the machine to take out that disk. Alice brings out her Chimchar. Palkia and Dialga collide, as Palkia throws Dialga to the ground. Brock and Nurse Joy lead the townspeople to a safer area of the town. Palkia uses Aura Sphere, while Dialga uses Draco Meteor which hits Palkia. Empoleon uses Ice Beam, Torterra uses Seed Bomb, and Infernape uses Flamethrower to block the rest of Draco Meteor from hitting them. Croagunk uses Poison Jab to block the final meteor of the attack, while Happiny is happy about that. Brock is relieved to see that as well.
Chimchar uses Flamethrower to make the hot-air balloon head to the top of the tower with Ash and his friends. Palkia uses Aura Sphere which Darkrai blocks and redirects with Dark Pulse, and causes a shock wave to hit everyone in the hot-air balloon. Piplup falls out of the hot-air balloon, as Ash brings out Staravia to rescue Piplup from hitting the ground hard and heads to the top of the tower. Dialga uses Draco Meteor, while Darkrai uses Dark pulse to block and redirect causing another shock wave to hit everyone in the hot-air balloon. Even though it redirected the attack, Darkrai was still hit by the attack. One of the meteors breaks open the basket of the hot-air balloon as Dawn almost falls out. Ash grabs her hand, but Palkia passes by causing a draft, making her slip and fall to the ground of the tower and hits the tower itself. Ash jumps onto part of the building, slides and jumps to the tower where Dawn ended up. Staravia brings Piplup to the tower, and Piplup hugs Dawn. The hot-air balloon floats away from the tower, as Staravia grabs Pikachu and gets away from the balloon. Chimchar uses Flamethrower so they could head toward the ground. Dialga uses Roar of Time which Palkia dodges, and Darkrai jumps in front of the balloon to block. The shock waves send the hot-air balloon out of control to the street, and Darkrai hits the ground hard. As the hot-air balloon heads towards the street, Alberto runs after it. Alice and Chimchar jump on to the ledge, and Alice slips and falls. Lickilicky tries to use its tongue to save her, but the grip slips and Tonio has to swoop in and grab her while hanging on to a Drifblim. Alice thanks Tonio and hugs him. Alberto looks behind him and notices that the street is now starting to disappear as well.
Ash brings out Aipom and Turtwig, and has them climb the tower with him. Aipom climbs the wall of the tower, while everyone else climbs the stairs to the top. The buildings surrounding the towers begin to disappear, as Palkia and Dialga keep on fighting each other. Dialga uses Draco Meteor, while Turtwig uses Razor Leaf and Aipom uses Swift to block the attack. Ash, Dawn, and the Pokémon continue climbing the stairs, as the park and much of the town continues to disappear. Brock goes into the pond to grab Darkrai, and along with Quagsire and Wooper, bring Darkrai out of the water. Alice checks on Darkrai, very similarly to how her grandmother checked on Darkrai a long time ago, as Darkrai remembers. Dialga and Palkia continue to clash, as Dialga misses with a Hyper Beam. Brock and Tonio notice that the town keeps on disappearing. Ash, Dawn, and their Pokémon continue going up the stairwell. Dawn brings out Buizel and Buneary to use Water Gun and Ice Beam to recreate steps for them to climb, after the other ones had disappeared already. Ash continues slowly up the ice-covered stairs as Pikachu tells Buneary that she did a good job and she blushes. The camera zooms out and shows how much the town is disappearing so far.
Meanwhile, Tangrowth uses Shock Wave, Torterra uses Seed Bomb, Infernape uses Flamethrower, Empoleon, Azurill, Marill, and Azumarill use Ice Beam, and Shinx and Luxio use Thunderbolt to try to stop the town from disappearing. Dialga uses Hyper Beam, while Palkia uses Protect to block. Palkia uses Aura Sphere, which hits Dialga. They clash against each other head on. Alice yells for them to please stop, as Darkrai remembers more of what Alicia said to it years ago. Dialga prepares to use Roar of Time, while Palkia prepares to use Spacial Rend to finish each other off. Tonio's computer shows that the attacks would have devastating results. Darkrai gets up out of the water while Sudowoodo tries to avoid the splash, and heads towards Dialga and Palkia. As Dialga uses Roar of Time and Palkia uses Spacial Rend, Darkrai gets in the middle of them and surrounds itself with a shadow orb to take the hits. The orb surrounds all three of the legendary Pokémon and traps them inside for the time being. The town continues to disappear, as the tower also starts to disappear even more. Ash looks on as Darkrai's orb continues to hold the Pokémon inside. Ash and Dawn continue up the stairs with their Pokémon. Inside the orb, Darkrai is looking exhausted while trying to keep it holding them inside. As Ash and Dawn continue up the stairs, Buneary uses Ice Beam to slow down the disappearing stairs.
The tower starts to really disappear, as Ash almost falls out of the tower and Dawn catches him, but they both fall out of the tower. Buizel uses Water Gun to send them to the top of another part of the building. The Pokémon continue up the stairs, as Ash and Dawn use another pathway to get to the music machine. Darkrai's orb starts shrinking, as Palkia and Dialga are able to get out of the orb. Ash and Dawn look out the window and notice the orb shrinking. The orb eventually completely disappears as Darkrai looks really hurt. Dialga uses Hyper Beam and Palkia uses Aura Sphere to hit Darkrai hard as it floats up into the air and disappears. Ash and Dawn continue running to the music machine, and finally reach it, as the Pokémon also reach the top as well. Piplup shows exhaustion after running around so much. Dawn pushes on a switch and pulls a disk out of the machine. Ash tries to replace it with the one they need, but it won't fit in the slot. Dialga and Palkia continue fighting as they prepare to use Roar of Time and Spacial Rend one last time. Tonio says to everyone that if those two attacks connect, the dimension will be completely destroyed.
At the top of the tower, Ash and Dawn try to figure out why the disk won't fit in the disk slot. Dawn notices one slot in the middle, tells Ash, and he places it right in that slot and pushes down on it. They both pull down on the lever to get the machine working, but it doesn't have enough power to work because everything was disappearing in the dimension. Dialga gets its Roar of Time ready, and Palkia gets its Spacial Rend ready to launch at each other, worrying everyone that it would now be the end. The town is looking like it is almost completely disappearing now. Staravia brings Pikachu up on top of the machine, and Dawn's Pachirisu climbs to the top of it. Pikachu uses Thunderbolt and Pachirisu uses Discharge at the machine so that it can start running again. The machine starts running as the music starts playing loudly across what's left of the town. Dialga and Palkia stop preparing their attacks and completely calm down, as the townspeople and all of the Pokémon all watch and listen. Pikachu stops his Thunderbolt out of exhaustion and looks to see what is going on, as the machine shines a bright yellow color and keeps working. The tower begins return to its normal state, as some flowers are shown to bloom on it. As the whole tower shines, it forms a shape of a very large yellow bird. Palkia's injury is finally fully healed. Dialga goes back to its own dimension. Ash, Dawn, and Pikachu ask Palkia to restore everything to the way it was before. Palkia restores the town to the way it was before and back to the dimension where it really is supposed to be at, as the dimension shines a bright white before doing so. Everyone is happy to see everything back to the way it is supposed to be.
As the sun sets, Ash and his friends look sad thinking they may never see Darkrai again. Alice remembers everything Darkrai did to help them, save her life twice, and sacrificed itself before disappearing. Everyone cries while worrying about not seeing Darkrai anymore, before walking away from the balcony. Ash notices a shadow on the wall of a cliff, as he walks back to the balcony along with everyone else. The shadow is shown to be that of Darkrai. Darkrai is shown to be on the very top of the towers and completely healthy again. Everyone is happy to see Darkrai, as Alice moves in closer to Tonio. The film ends with the camera zooming in on Darkrai and his eye glowing green as the screen fades out to black.
In the end credits, it shows the aftermath that occurs after everything that happened, such as the Pokémon Contest which Dawn competes in where Allegra wins. Not too long after, it shows Dialga going towards its next destination awaiting a battle, which will start the next adventure Ash, Dawn and Brock will face.