The movie opens with strands of DNA. Pokemon such as Darkrai appear in bubbles within the DNA, subtly hinting that all Pokemon are related to each other and ultimately Arceus. The scene then shifts to an ocean with Kyogre and Manaphy swimming, followed by Lugia who jumps out of the water, flies high into the sky, and then dives back in. Articuno, Zapdos, and Moltres fly by as well, and then the camera zooms to some rocks by the ocean where Entei, Suicune, and Raikou are standing. We also see Groudon roaring.
A Garchomp and Milotic are fighting in an arena, launching attacks at each other. Who owns them? Cynthia and Palmer! They are battling each other.
Grass Pokemon are sitting in a field. In a night scene, a Dusknoir comes out and attacks Pikachu with a Will-o-Wisp. Pikachu and Piplup attack the Dusknoir, creating an explosion.
The typical intro music calms down and transitions to the "legend theme" used in the Darkrai and Shaymin movies (the slow piano theme from when Tonio is reading Gaudy's diary). Dialga and Palkia are seen fighting in a flashback straight from the Darkrai movie. As they fight, there is a cut-scene to the Space-Time Machine. Dialga and Palkia's dimensional spheres clash against each other, symbolizing their interaction. Another flashback occurs in which a solar eclipse is seen. Arceus' plates circle around the sun and its 1000 arms spread across space, with the camera zooming in to Arceus in a bubble. A conversation between it and a human in the past echoes in its mind. Whatever happened in the past, Arceus has been dwelling on it and is full of rage. The camera zooms down to Earth and the Pokemon logo rises out of the ground. The music playing is an updated version of the intro music from the Deoxys movie.
The movie opens with Ash, Dawn, Brock, Pikachu, and Piplup walking through a large grass field. They come across a river and decide to go swimming. Ash and Dawn are like brother and sister and splash each other repeatedly. While in the water a couple of watermelons float down from upstream. When they pick one up, a boy and girl with blue hair appear and point to some nets in the water. The watermelons are being cooled in the river, but a few escaped. The two characters tell Ash that if he wants the watermelons, he will have to battle them. Ash as usual accepts, and so he and Dawn face off against them in a 2-on-2 battle. An updated "High Touch!" song plays in the background. It's Pikachu and Piplup vs. Beautifly and Heracross. Piplup gets launched into the air by Heracross' horn and Beautifly greets it, charging up a Shadow Ball to fire. Pikachu jumps into the air and smacks the Shadow Ball right into Beautifly's face, and then Piplup uses Whirlpool on both of the opponent's Pokemon, knocking them out. After the battle, everyone and their Pokemon enjoys the watermelons.
In the next scene, Ash and crew walk up to a lake that sits atop a tall mountain. Suddenly rifts in the sky and water form, and giant water tornadoes grab everyone except Brock, who pulls Dawn and Ash out. Pikachu and Piplup fly high into the tornado, which is heading into a spacial rift. Pikachu holds on to Piplup as it fires Bubble at the tornado to prevent them from getting pulled in. Sheena and Kevin jump out of nowhere and observe the situation. Sheena holds out her hands and prays, and Dialga appears out of its own dimension, knocking Pikachu and Piplup out of the tornado. It fires a Roar of Time at the tornadoes and disintegrates them (the shot of it using Roar of Time is directly from the 10th movie - reused animation). Brock of course hits on Sheena, grabbing what he thinks to be her hand. It's of course Croagunk's, who jabs him with poison and then drags him off-screen.
A rift from the Reverse World opens up in the lake and Giratina flies out of it, attacking Dialga with a Will-o-Wisp. The two exchange fire for a while as the same music from when they were fighting at the beginning of the 11th movie plays. Sheena clasps her hands together, closes her eyes, and we see her enter into a psychic connection. She recites, "Conquer it... the laws of time and space!" In the connection, Giratina is completely red with rage. The area around it is red as well. Sheena attempts to communicate with it, but Giratina's rage thrusts her backwards (in the psychic time), causing the connection to break. It's still angry from the events of the 10th and 11th movies and Sheena's powers are unable to calm it. Ash runs into the lake and yells at Giratina for it to remember him. At first the Pokemon don't even notice him and he is splashed around a little, but eventually Giratina sees him. The Pokemon stares at Ash intensely, remembering how he rode him it the Shaymin movie, and then calms down and stops the attack on Dialga. Dialga calmly rises into the sky and circles around for a while. Sheena again uses her powers on Giratina and the scene shifts to the psychic time; this time, the area around Giratina is blue and its colors are normal. Sheena explains that Dialga is not its enemy, and Giratina makes a few surprised expressions. After Sheena is done with it, Giratina goes back into the Reverse World. Sheena also jumps down to where Ash is and checks out Pikachu, stating that it has a strong bond with its Trainer.
In another dimension, we see a giant rift flow across space. Back in the real world, another water tornado forms and the wind becomes violent. Dialga gets captured in the tornado and can't escape. A mini black-hole also forms in the air and tears a tree in half, which almost hits Dawn; however, Kevin jumps in and grabs her out of its path. Palkia appears out of its own dimension, thrusting a Spacial Rend into the air to destroy the water tornado. Dialga seems to thank Palkia for helping it (the two exchange light roars briefly), and then Sheena again uses her powers to resolve any remaining conflicts both Pokemon may have. Both Dragon Pokemon then leave back into their own dimensions.
Ash and crew follow Sheena and Kevin into a room within the mountain they are on. Sheena shows them the Space-Time Machine, explaining that the five spheres orbiting on it represent our world, the Reverse World, Palkia's dimension, Dialga's dimension, and Arceus' dimension. Ash asks if Arceus is a Pokemon, which Sheena confirms. Sheena explains how she and Kevin were investigating the legend of Arceus and their town's history. A flashback shows them outside of Alamos Town as Palkia was putting the city back where it belonged in the 10th movie, followed by a flashback of the two in front of the glacier in the 11th movie after Zero's ship crashed.
The Space-Time Machine fluctuates. In space, we see Arceus beginning to awake - its face is full of rage. It's encased in some sort of bubble with a thousand or so golden strings surrounding it (its 1000 arms?), and breaks out of the bubble. It stands in front of the camera with an angry stare, glowing gold. Its 11 plates then circle around it and absorb into its body. It heads off.
Back in the room, Sheena and Kevin show the kids the legend of Arceus and their town, which appears on a waterfall display as stylized stained glass. Arceus stopped a meteor from crashing into the planet many years ago, but lost its plates in the process and was severely injured. A human named Damos helped Arceus recover by returning one of the plates to it. As a result of the meteor, Michiina was destroyed. Feeling pity for the humans living there, Arceus took its Water, Ground, Grass, Electric, and Dragon plates to form the Life Jewel and gave it to Damos, which used its power to transform Michiina into a fertile land. Sheena then explains that Damos betrayed Arceus by not returning the jewel, which causes Kevin to close his eyes in guilt. She tells them that Damos ordered Electric Pokemon to attack Arceus, and that Arceus fled back to its own dimension to recover but that it would one day return. Ash and crew remark how evil Damos is as Sheena walks off-screen. She opens up a case that is holding the Life Jewel, revealing that she has it, and tells the kids that Damos was her ancestor, which causes them to stop bashing him out of embarrassment.
The Space-Time Machine fluctuates violently. Sheena turns around frantically and announces to everyone that Arceus has arrived. Outside, dark clouds form and a golden rift opens up in the sky. DNA strands flow out of the rift and Arceus appears out of it rather quickly. It wastes no time using Judgment, which it launches into the sky like fireworks. The attack explodes and then rains down on Michiina, destroying buildings, bridges, the mountain, its temple, etc. The city is a complete wreck.
Arceus begins to charge another Judgment. However, the camera cuts to Damos' feet running. Arceus stops the Judgment and looks down at its temple, seeing Damos. Damos is not actually there, but Arceus senses that someone resembling Damos is coming toward him. Arceus pauses and looks up the mountain. Sheena runs out to Arceus, presenting him with the Jewel in a rather calm scene. Arceus calms down and comes closer to examine the Jewel, which Sheena is very emotional about giving back. Team Rocket is on the sidelines, debating rather comically about who should go steal it. Since they are in the presence of Arceus, however, they ultimately decide not to take it since they might get beat up badly.
Arceus seems grateful to have the Jewel back. However, when examining it, it completely crushes it with one of its hooves and declares it a fake. Everyone is shocked, Team Rocket especially. Sheena pleads with Arceus but it's no use; it launches a Fire-type attack at them, which tears into the mountain. Team Rocket falls through the top of the mountain into an underground lake, and is then pulled down into a river, which turns out to be feeding the huge waterfalls flowing out of the mountain. They go blasting off down the waterfall.
Arceus launches another Judgment into the air. As the energy balls begin to rain down, Dialga and Palkia simultaneously emerge from their dimensions and use Protect, blocking the attack from hitting the humans. Arceus becomes even angrier, asking its two creations why they are protecting the humans. It launches a Fire-type attack at Palkia first, which uses Protect again, but the attack explodes on it and pushes it into the mountain. The attack is still going and hits Dialga, who is knocked into a pillar and collapses. Kevin tells everyone to run as Arceus charges another attack. He stands in front of the attack to protect everyone, but Giratina emerges from its dimension and takes the blow. Arceus fires Blizzard at the three Dragons in reaction: Dialga is hurt even more, Giratina is hit, and Palkia is using Protect and is unaffected.
Giratina fires a Will-o-Wisp at Arceus, but Arceus changes its type to Fire and resist the attack completely. Dialga tries too, but Arceus resists it as well. Arceus tries to attack the humans again but Pikachu zaps it, which actually hurts it. Kevin explains that since Arceus is missing the Zap Plate, it can be hurt by Electric attacks. Palkia steps in and uses a watery attack on Arceus that traps it in a bubble - Palkia is using the powers of space to encase Arceus in a mini-dimension, which it cannot escape. Dialga, who is still on the ground and weak, stares at Sheena. She looks up at it, and suddenly Dialga's eyes glow. Everyone begins to disappear except Kevin. The next scene shows them traveling through a blue tunnel; Dialga is transporting them through time.
In the past, it is night and an eclipse is occurring. Arceus appears out of the sky and floats down to a temple lit by fire to meet Damos, who is supposed to return the Life Jewel to Arceus on this day. The camera angle cuts off Damos' face, obviously because he is being controlled. Damos is holding the Jewel and tells Arceus to come inside, so it follows him into the heart of the temple. Damos places the Life Jewel in the center of the temple. Sheena and everyone else is observing the scene from the top. Suddenly, several dozen Pokemon wearing Gishin's machines attack Arceus with Electric attacks. Arceus doesn't understand what's going on and asks Damos what he's doing, and we can see that Damos' eyes are missing their shine, meaning he is being controlled. Damos walks up to the top where Gishin, his Heatran, and his Bronzong are standing and releases the candle chandelier hanging from the top of the temple, which crashes down on to Arceus. Boulders are also released, completely burying the Alpha Pokemon. While all of this is happening, the Pokemon are still firing Electric attacks. Arceus is hurt severely but blasts the boulders away with a windy attack. It struggles to reach for the Life Jewel so it can regain its Zap Plate, but it realizes it is a fake and launches a Judgment into the temple. It blasts all the walls in and knocks Damos and Gishin to their deaths. The Jewel is contained in a staff held by Gishin and is buried in the rubble. Sheena and crew also fall, but she prays to Dialga (who is still in the present) to send them back even further in the past. Dialga again whisks them away.
In the present, Dialga's side strips are glowing blue but its eyes are closed, indicating that it is very weak. Giratina, Palkia, and Arceus are still fighting. Dialga apparently faints, though it is still conscious. Giratina comes up behind Arceus with a Shadow Force but the attack fails to connect. It then tries to fire another attack, which Arceus resists. The town, mountain, and temple are further destroyed. Team Rocket is washed ashore in all of the fighting and a staff is stuck in Jessie's clothing. She uses it as a cane.
In the past, Sheena and crew are immediately surrounded by Heatran, Bronzong, and guards that are missing the shine in their eyes. Dialga sent them back to the afternoon of the same day. Gishin orders Bronzong to use Hypnosis on everyone except for Sheena, which hypnotizes them. Notched-Ear Pichu is observing the situation from afar and goes inside a building. The next scene shows a bag being thrown into a prison by controlled guards, which contains Piplup and Pikachu. Both are surrounded by strong, sleeping Pokemon. They are the same Pokemon that will attack Arceus later in the day. A Manectric threatens the two for making so much noise and then goes back to sleep. Pichu then comes in through a hole and tells them to come with it. Pikachu and Pichu rub their tails together to greet each other, and Piplup tries to do the same but gets shocked. They all head back the way Pichu came in.
Ash and crew are in jail and become unhypnotized as they are locked in. An old man outside the cell explains that Gishin used his Bronzong to control them. A little bit after, they see that Damos is in the cell with them. Ash yells at Damos for what he has done, but Damos of course doesn't know what he is talking about since it hasn't happened yet (not to mention he was being controlled by Gishin's Bronzong when he did it). Ash shows Damos Poke Balls, his Monferno, and tells him that these creatures are called Pokemon. However, Damos only knows them as "monsters."
Sheena is having quite a lovely dinner with Gishin and his two Pokemon. Gishin is interested in what Sheena has to say about Arceus, since earlier, she was trying to tell the guards what will happen in the future. Gishin listens as Sheena explains that Damos must surrender the jewel to Arceus to prevent Arceus from being hurt and the destruction that will occur in the future.
Meanwhile, Pichu, Pikachu, and Piplup are traveling in some sort of tunnel. Piplup smells some food cooking and heads in another direction, which leads to a kitchen. A man is ordering a Chikorita to cut a vegetable and a Cyndaquil to keep fueling a fire, and when they try to rest, he yells for them to keep working. Both Pokemon are tired and it is obvious they don't like the man. Piplup unintentionally falls down from the tunnel, causing pottery to fly everywhere. One gets stuck on its head, which causes Piplup to look like some sort of monster. He walks toward the man while blinded, causing the man to walk backwards in fear. He hits a shelf and a pot falls off, smacking him in the head and knocking him out. Pichu and Pikachu use Iron Tail to break the machines that are strapped around Chikorita and Cyndaqul, and everyone escapes from the kitchen as the man begins to come-to.
In the present, Team Rocket has again fallen through the mountain and encounters pottery encased in mud from an old kitchen. Meowth tries one on. Palkia is able to again subdue Arceus by trapping it in a mini-dimension.
Back in jail, Damos is offended at what Ash and crew were saying and says that it helped Arceus long ago. The following flashback took place for over 10 minutes. Damos is walking across desolate land at night and it is lightly snowing. Huge meteors strike and destroy the land, and as Damos looks up, an even larger meteor approaches, which is the source of the large meteors already striking. Damos shakes his head in disbelief and fear at the Earth's impending death. Suddenly, Arceus appears out of its dimension and flies up to the meteor. Its plates leave its body and circle around it, forming a strong barrier around it. Arceus then rams the huge meteor and is like an ant in comparison to it. The ensuing explosion is the largest that has ever occurred in the anime, and the meteor completely dissolves as it collides into Arceus. From afar, we can see the meteor is disintegrating into the atmosphere. Arceus makes a painful grunt and loses all of its plates in the process. The remains of the meteor crash down, causing the wild Pokemon and the few humans living on the land to run into caves for cover.
Back on the ground, Arceus appears dead. Pokemon are surrounding it to protect it, fearing for its safety. All of the Pokemon are weak to Ice and are being weakened by the falling snow but don't care. Damos uses the same psychic power as Sheena and attempts to communicate with Arceus, but there is no light emanating from it. Damos tries harder and sees a small amount of light. The light gathers together and begins to wander away from Arceus' body - Damos understands that he must follow it. In doing so, he discovers one of Arceus' plates; it is about the size of a slab of granite. When he brings it close to Arceus, its mandala begins to light up and the plate floats out of Damos' hands. Once the plate inserts itself into Arceus' body, the green jewels on its mandala blink repeatedly and the other plates hover out of the ground and fly back to it. After the last plate absorbs itself into Arceus, its body lights up and beats like a heart. As this is occurring, the sun is beginning to rise. Arceus rises into the air as the sun's light flows out from behind the mountain and the music swells, creating a rather beautiful (and arguably religious-looking) scene.
Arceus asks Damos for his name and thanks him. It looks upon Michiina in pity, but shows Damos through his (Damos') psychic power what Michiina could look like. Michiina is already a barren land, and the meteors made it worse, but Arceus shows him a vision of it covered by plants, trees, and water. It then calls out its plates, removing five of them - Water, Ground (earth), and Grass because they are the basic elements of the land, Electric to hold them all together, and Dragon to increase their overall power. Arceus then creates the Life Jewel, giving it to Damos. Damos raises it into the air, and the land below instantly flourishes. Damos is teary and thanks Arceus again. The next scene shows Michiina later on with crops and more people than before. Damos says hi to a man and his Tauros, who is plowing a field. The man tells Damos the progress on the crops and Damos wishes him luck. Later in the day, Arceus tells Damos it is going to leave now and tells him to give the jewel back during the next eclipse when he awakens. As Sheena and crew witnessed earlier, of course, this did not happen. Back in the jail cell, everyone now understands that Damos is not evil.
Back at dinner, Heatran walks along the wall and Bronzong hovers next to Gishin. Sheena is still talking about the future and what will happen. Gishin tells her he understands what will happen and that she can have the Life Jewel. He shows her the jewel inside of a staff but then walks into the corner, removes it, and hides it in his clothes. He hands the empty staff to Sheena, who will deliver the jewel to Arceus that night.
Piplup, Pichu, and Pikachu are still running around. They pass by a bunch of barrels being filled with hot metal. They eventually find a room where the jail keys are hanging. Piplup strings Pikachu and Pichu down but they can't get the keys. Suddenly the door knob begins to shake and the three Pokemon look toward its direction in a panic. Who walks in? A Totodile! Pichu tells it something, Totodile smiles, and then it Water Guns the keys and the Pokemon on to a pillar. They now have the key they need, and Totodile walks back out the door.
Back in the present, Arceus has seriously destroyed everything in the area. As Team Rocket sees Arceus and Giratina fighting, a stray attack from Arceus rips open the side of the mountain. Arceus uses Judgment again.
Back in the cell, a candle flickers and Damos senses someone is coming. It's his friend Pichu with the keys! Notched-Ear Pichu hands them to Damos and he thanks the Pokemon for a good job. The old man outside, who is actually the jail guard, pretends not to see them leave. Damos hands the keys back to him and everyone heads off to the temple.
It is now night and Arceus enters into our world, going down to the temple to get the Life Jewel from Damos. Sheena greets him inside, telling Arceus that it is giving the Jewel to him in place of Damos. When she opens the staff, the Jewel is of course missing since Gishin removed it. As soon as this is revealed, Gishin's Pokemon attack Arceus with Electric attacks. It's the same thing all over again, except this time water from the mountain is drained into the temple, knocking Arceus to the floor, and then hot metal is poured on to it for even more damage. Sheena doesn't know what to say and yells at Gishin to stop. Arceus can't escape the metal, which hardens. Its eyes turn red in anger as it understands that it is being betrayed by humans. It fires off an attack, which causes Sheena to fall. However, Damos grabs her. She is struggling with him because she thinks he is evil, but he uses his psychic powers to explain the whole situation to her, and the two smile at each other.
Damos and Sheena attempt to run up to the top of the temple to stop Gishin, but a bunch of liquid metal is rushing toward them. Brock appears out of nowhere and orders Sudowoodo to use Hammer Arm, which destroys the floor and causes the metal to fall below. Ash tells Brock he's going to run up to take the Jewel back from Gishin. He meets Dawn at the top, but Heatran is on the ceiling and shoots off a Fire-type attack at them. Bronzong also uses some sort of beam attack. The kids are knocked to the floor, and then Bronzong uses Gyro Ball, missing his targets and returning back to Gishin. Heatran is about to fire another attack when the Johto starters and Rattata appear out of a tunnel and stop it.
Arceus is still being attacked by the Electric attacks and is almost completely buried by the metal. Sheena and Damos use their powers in tandem and tell all the Pokemon to stop hurting Arceus. The Electric attacks stop one-by-one until no Pokemon are attacking, and Heatran and Bronzong also stop attacking Ash and Dawn. Gishin doesn't know what to do and Pikachu removes the machines controlling them. All of the Pokemon face Gishin in a threatening manner.
Damos and Sheena are trying to communicate with Arceus. Arceus' rage forms a barrier around it in the psychic connection and both can't break through it. Sheena is thrust away in the connection, but Damos is able to hold his own. His blue eyes are striking against the intense red rage surrounding Arceus in the psychic time.
Ash fights Gishin literally but can't get the Jewel away from him. He struggles with him and tries to grab the jewel out of his hand. In the struggle, Gishin drops the Jewel and it begins to role away. Chikorita attempts to grab it but fails, but Ash jumps down and catches it with his legs. It's slipping out, so Pikachu goes under him and catches it again.
Damos can't break through Arceus' rage, so he jumps from the top of the temple down to Arceus (in psychic time). The rage is so strong that he falls slowly.
Ash and Pikachu try to present the Jewel to Arceus below, but it is completely frozen, as if it is a dead carcass stuck in tar. It is alive however, but not moving, and its eyes are open and completely red but not responding. Another set of liquid metal pours down on Arceus, covering it up to its face. Ash, Dawn, Pikachu, Piplup, and Sheena begin to disappear as this happens. Apparently, Arceus being alive lead to them being alive, so if Arceus dies, they die in the future. Pikachu completely disappears as Ash screams, and so does half of Ash. All of them become quite emotional of the situation. Ash is holding out the jewel to Arceus, his hand shaking, but nothing is happening. Another batch of metal completely covers Arceus. Gishin also laughs at Dawn as she begins to disappear, stating that he wins and they lose. All of the Pokemon watch what's happening and don't know what to do.
In the psychic connection, Damos reaches the rage bubble surrounding Arceus. He struggles and struggles to break though it and finally thrusts his hand through it. He touches Arceus' head, screaming "ARCEUS!!" There is total silence, and the red color surrounding Arceus completely disappears. Arceus raises his head and looks completely normal, saying "Damos?" As this happens, the jewel floats out of Ash's hand toward Arceus and breaks down into the five plates, absorbs into Arceus' buried body. A beautiful golden light surrounds Arceus and shoots up into the air, and Arceus is able to break free from the metal. All of his plates circle around him and he is completely calm. Ash and everyone else is back to normal and Pikachu reappears. Arceus asks Ash and Pikachu their names since he knew they were trying to return the jewel to him.
However, the liquid metal overflows from the top of the temple and pours down even harder than before, destroying the walls. Boulders also crash down, and all the Pokemon and humans begin to fall. Arceus slows down everyone and everything's fall, disintegrating the boulders and gently pushing everyone back up. He appears to be wearing his Flying-type plate as he is doing this, since he's light blue and everyone is floating as if they are flying. He then changes to Grass-type, sending out a wave of green that dislodges all of Gishin's machines from the Pokemon that were attacking him with electricity.
Gishin is standing on top of the temple still. He says to himself that because the Life Jewel returned to Arceus, Michiina will become a wasteland again. The only reason he did all of this was out of fear of Michiina returning back to how it was.
Outside, Damos apologizes to Arceus, but Arceus says he understands what happened and that he knows Damos is good. He then floats up into the sky as the first part of the "World of Pokemon" theme plays and goes back to his dimension. Sheena tells everyone that Dialga is calling them back to the present, and so they are transported back. Damos and Pichu look out over Michiina, which is completely normal.
In the present, Dialga, Palkia, and Giratina are all laying on the ground in pain. Ash and crew return to a rather calm scene, and to the audience, it would seem that since now Arceus was calm in the past, it is calm now. However, it becomes quickly apparent this is not the case. Arceus fires a large Judgment into the sky, which begins to rain down. Ash in almost a tearful cry screams "ARCEUS!!!" and the camera zooms up to Arceus' eye. He remembers them... he says, "Satoshi... Pikachu..." Quick flashbacks from the movie play in Arceus' eye, and it is reminded that everything is okay now. Arceus thus freezes its Judgment in mid-air. The clouds overhead begin to break up and golden sunlight rains down on the land, hitting Dialga, Palkia, and Giratina. The three Dragons then rise into the air behind Arceus, and everything is restored back to how it was before Arceus destroyed everything. As one of the bridges is restored, Totodile, Cyndaquil, and Chikorita are shown to be engraved on it.
Brock asks everyone why Michiina did not become a wasteland again, and Sheena redirects the question to Arceus. Arceus explains that it wasn't the Life Jewel that kept Michiina beautiful and fruitful, but the hard work of the humans and Pokemon of Michiina.
Kevin finds everyone and runs to Sheena and the two embrace each other, causing Brock to freak out. Arceus floats down next to the humans and watches as its three creations depart back to their own dimensions. Everyone screams goodbye to them and Ash thanks them for everything.
A legend written on a stone tablet that was in the Time-Space Machine room at the beginning of the movie has now completely changed and is displayed prominently in front of Arceus' temple. It shows Ash, Dawn, Brock, the G/S starters, and Sheena. Sheena reads the legend out loud, and the scene shifts to Damos in the past, who finishes reading it (since he wrote it). It says, "To the children from the future who taught me to have faith: I'm driven by the goal of making your future a wonderful place. I wonder what kind of place your future is." Sheena tears up in the present and says "Damos..."
Arceus calls to Ash and turns toward the sunset, saying that their world is beautiful and flies off (perhaps answering Damos' question). Ash and crew yell to it goodbye and it flies high into the sky, going back to its dimension. Everyone turns to each other and smiles.
In the ending credits, we see the stylized stain glass depictions of the Arceus legend and how it has changed to reflect the events of the movie. Ash and crew are riding in a truck with the two blue-haired kids from the beginning of the movie. Team Rocket steals a watermelon only to discover that it is a Voltorb, which explodes and blasts them off. Ancient artwork shows people and Pokemon working in Michiina, including Heatran and Bronzong. The artwork transitions to animation and we see that Gishin is working with Damos in a field, though Gishin doesn't look too happy.
Back in Alamos Town, Alice and Tonio are riding in her hot air balloon as the Baron bikes by in his own hot air balloon. Darkrai is in the distance watching, and returns to the ground. Zero is in jail. Newton visits him with a hologram (like the one in the first movie with Nurse Joy). Out pops Infi, which Zero is excited to see (it's drawn in 2D - the only appearance Infi has in traditional animation). Newton was obviously able to recover her program from the ship. Shaymin is also seen sitting in a tree and comes out to the sunrise.
Palkia, Dialga, and Giratina are flying around in their dimensions, as is Arceus. Ash and crew are walking. They rest in an igloo at night. Next they are eating next to a train as the mother and daughter from the Lucario movie intro walk by. The last shot shows them next to a body of water by a bridge, leaning against the railing. The camera pans up to the sky and the movie ends.
The teaser trailer for the 13th movie begins immediately! Lugia is flying down and dodges a Fire-type attack from Ho-Oh, and then circles around and fires a Hyper Beam back at it. Ho-Oh flies up from the right and launches another Fire attack, and Lugia flies in from the left, launching an Aero Blast. The attack looks like blue electricity mixed with wind. The two attacks collide and create an explosion. The "Pocket Monsters: Diamond and Pearl, Platinum" logo pops up, and then "2010" appears under it.