Thousands of years in the past, the legendary Alpha Pokémon Arceus came to Earth to retrieve the "Jewel of Life" that it had loaned to a man named Damos. Damos however betrayed Arceus and attacked it with a large army of Pokémon. After presumably killing Damos in its counterattack, Arceus went to sleep, vowing to judge all humans when it next returns based on Damos's actions.
After walking through a patch of long grass Ash and his friends reach a beautiful area called Michina Town. Deciding to take the chance to relax, everyone sends out their Pokémon and make the most of the idyllic surroundings. As they are playing in the river, three watermelons float towards them. The gang looks forward to eating them when a boy named Kato and a girl named Kiko come to claim the watermelons, as they belong to them but were washed away when they were left in the river to cool. Everyone is disappointed, so Kato and Kiko make them a deal... Ash and his friends can have them if they can beat them in a Tag Battle. Taking on Kato and Kiko's Heracross and Beautifly, Ash and Dawn use Pikachu and Piplup. Although the battle is hard fought, the teamwork between Trainers and Pokémon shines through and Ash and Dawn win, but decide to share the watermelons with Kato, Kiko and all the Pokémon. Later, Kato and Kiko recommend that they go Michina Town's famous ruins.
Ripples start to emerge from another part of time and space, which causes a spatial distortion to open near the gang. Although Brock is able to hold on to Ash and Dawn, Pikachu and Piplup are swept away and although Piplup is able to stop the two from being immediately sucked in by using BubbleBeam to stop the momentum, it appears all is lost for the two. Suddenly a girl named Sheena arrives and calls Dialga, the Pokémon that rules over time, to come and help. Dialga saves Pikachu and Piplup from being sucked into the distortion, and after returning the Pokémon to their Trainers then usesRoar of Time to close it up. Everyone is amazed to see the legendary Dialga hovering above them, and even more so that Sheena was able to summon and communicate with it.
Suddenly, another ripple starts to emerge from the river but it isn't another distortion... it's Giratina! The Renegade Pokémon immediately attacks Dialga, still enraged over the damage done to its world. Everyone can't believe that Giratina is still after Dialga and plead with it to stop. Sheena attempts to use her special ability to touch a Pokémon's heart to reach and calm Giratina, however Giratina is so full of rage that her attempts fail and she is caught by her partner Kevin. Ash runs towards where Giratina is battling Dialga in the river and pleads with it to stop. Giratina stares at Ash for a few seconds, and remembers that Ash was the person that saved its life before. Giratina's anger dissipates, and Sheena takes the chance to reach Giratina using her powers and convinces it that Dialga has been misunderstood and shouldn't be battled. Giratina understands and immediately returns to its own dimension.
Sheena and Kevin introduce themselves to everyone, and Sheena explains that she has the ability to connect with a Pokémon's heart and communicate with them. Sheena is especially curious about Ash and Pikachu, as she recalls a legend that a Thunder Creature and its master once changed the course of Michina Town's history and asks the gang to accompany her. Naturally Brock moves in with yet another misguided romantic attempt claiming that Sheena helped to remove the pain that was caused by a scraped elbow... unfortunately for Brock, the pain is delivered right back courtesy of Croagunk'sPoison Jab. As Croagunk drags the truly hopeless romantic Brock away, suddenly another distortion appears and Dialga is caught in the resulting water spout traps Dialga and the distortion starts to drag it away. Suddenly another portal appears and from it emerges Palkia, the Pokémon that rules over space. Palkia uses Spacial Rend to free Dialga and close the distortion, and Sheena communicates with them both and uses her amazing powers to end the conflict between them for good. Both Pokémon, having settled their differences, return to their own dimensions.
Nearby, everyone is being watched by none other than JessieJames and Meowth. Jessie is very excited to have not only seen the rulers of space and time but also a woman who can control them. Jessie attempts to use her charm to touch Meowth's heart, but it's Meowth's Charm that ends up doing the hypnotizing, as Jessie falls in love with her own reflection which is shown on the shiny surface. James and Meowth can only sigh for their one-track minded teammate.
Inside the ruins, Sheena and Kevin show everyone the Time-Space Axis, which they use to monitor disruptions in the space-time continuum. With the help of the Axis, Sheena and Kevin were present when Palkia returned Alamos Town to its correct location, and also were able to investigate the glacier that was damaged during the conflict with Zero. Sheena and Kevin explain the various worlds that exist...first there's the human world, which is supported by Giratina's Reverse World, then there are the Temporal and Spatial Worlds inhabited by Dialga and Palkia... and these were all said to have created by the legendary Pokémon... Arceus. Recently, Arceus has begun to awaken which has caused ripples in the space-time continuum. As a result, the Temporal and Spatial Worlds intersected with each other. Both Dialga and Palkia believed that the other had attempted to invade their territory which caused the battle that almost destroyed Alamos Town. As a result of the battle, the Reverse World was damaged causing Giratina to be drawn into the conflict. Sheena explains that she was unable to reach Giratina's heart due to it being filled with anger.
Meanwhile, at the center of space-time, Arceus awakens and begins its journey to the human world...
Although the conflict between Dialga and Palkia has been resolved, according to the Axis it is nearly time to Arceus to emerge... and deliver its Judgment upon the world. Sheena tells the legend that once the planet was in serious danger from being destroyed by meteorites. However Arceus helped to destroy the meteorites, but in the process lost the sixteen Life Plates that normally helped it defend against any possible attack. Arceus's death appeared to be inevitable when a man named Damos helped Arceus retrieve the Plates and ensured its survival. At the time Michina Town was a desolate wasteland but Arceus, in gratitude at being saved, used five of its Plates to create the Jewel of Life which helped transform the wasteland into a paradise. Arceus put its own life at risk to create the Jewel of Life, however when the day came that Damos was supposed to return it he instead betrayed Arceus and attacked it. He believed that returning the Jewel of Life would doom Michina Town and cause it to return to its previous state. Arceus, filled with unspeakable fury at being betrayed by Damos after risking its life to help him, destroyed the shrine but was injured so was forced to sleep and recover but it was known that eventually Arceus would return and unleash its wrath upon the planet. Sheena then tells everyone an astonishing fact; Damos is her ancestor. However her plan is to try to calm Arceus by returning the Jewel of Life which is in her possession. Suddenly the Time-Space Axis begins to chime and shake violently, which means only one thing... it is time for Arceus to emerge.
Arceus arrives in the human world and, still filled with fury over its previous betrayal, begins to pass down its Judgment. It sends a sphere into the air, from which several energy beams emerge and begin to destroy Michina Town and the ruins. Suddenly, Arceus sees Sheena and she apologizes for Damos's despicable actions in the past and humbly returns the Jewel of Life. Arceus calms briefly before suddenly becoming even more enraged than before as it steps on the Jewel of Life shattering it into pieces. Arceus furiously tells Sheena that the Jewel of Life was made up of itself and cannot be broken... the one Sheena had possession of was a fake. Taking this as a sign that humanity cannot possibly be trusted, Arceus completely destroys the ruins, sending Team Rocket (who has rather grand plans of stealing the Jewel of Life and capturing Arceus) falling into the river below. Michina Town continues to crumble beneath Arceus's might until Dialga, Palkia and Giratina return to stop it. Palkia is able to subdue Arceus long enough to allow Dialga to send everyone but Kevin back in time to alter the past.
When the group arrives, they see Damos enter the temple with the Jewel of Life on a staff. Following him, they all witness as he betrays Arceus as already known, however, it becomes apparent that another man who is dressed in a red toga and controls a Heatran and Bronzong wearing strange armor is also involved. Furthermore, Damos appears to be under hypnosis of some sort. When Arceus violently counterattacks, Ash and his friends nearly fall to their deaths along with Damos and the other man, but Sheena quickly prays to Dialga again and manages to get it to send them back a bit further in time.
Meanwhile, in the present day, Arceus is gaining the upper hand in its battle against the creation trio and the strain of sending the group back in time causes Dialga to faint.
Ash, BrockDawn and Sheena arrive in the afternoon several hours prior to Damos's betrayal. Sheena becomes alarmed when she realizes that Dialga can no longer send them through time, and things get worse when a group of armed soldiers surrounds them. The man in the toga appears with his Bronzong and has it use Hypnosis on everyone but Sheena. The girl attempts to warn him of what is going to happen, garnering the man's interest, so he orders his guards to take the others away while he interrogates Sheena.
Ash, Brock and Dawn are thrown in a jail cell guarded by an old man and soon realize they are sharing the space with Damos, who appears jovial and in control of himself, unlike what had previously been seen. The group's initial reaction to him is overwhelmingly negative, to which he takes offense. The gang explain that they're from the future, which Ash demonstrates by briefly sending out Monferno. Damos is amazed by the Poké Ball, technology that doesn't exist in this time, and believes their story and starts to tell them his. Damos explains that in the past, he was traveling through the wasteland that was Michina Town when he witnessed the destruction of the meteor by Arceus, and found it when it was nearly killed by losing the Life Plates. After searching the area, he found one of the Life Plates and returned it to the Alpha Pokémon. As a result, Arceus began to heal and all the other Life Plates were able to return to their owner, completely restoring Arceus's strength. Although Arceus was healthy, the same couldn't be said for Michina Town. The land was barren and lifeless and it appeared that Damos and the other inhabitants wouldn't survive the coming winter. Arceus, wishing to help the person that had helped it when it was near death, decided to grant Damos the use of its Plates. First it handed over the Plates that harnessed the power of GroundGrass and Water then bound them together with the power of Electricity and then increased their powers with the force of the Dragon and formed the Jewel of Life. With the Jewel of Life, Michina Town was soon flourishing with life. Crops were plentiful and the entire area was a beautiful sight. Arceus returned to visit and was happy to see Damos doing so much good, but explained that the Jewel of Life must be returned at the date of the next solar eclipse as its life was in danger while it was parted from any of its Life Plates. Damos then built a shrine to Michina Town's savior, and ends the story insisting that he has no intention of notreturning the Jewel.
After hearing that they were imprisoned by a man with a Bronzong, Damos identifies him as Marcus. Thinking back, Brock realizes that Marcus and Bronzong were present at the scene of Damos's betrayal and theorizes that Marcus was the real mastermind and that he was controlling Damos through Bronzong's Hypnosis.
Marcus, meanwhile, is hosting Sheena at a dinner. She explains everything to him, that Damos is going to betray Arceus and cause the world to be placed in danger, so Marcus agrees to assist her in stopping him. He then walks over to an area obscured by his Heatran and secretly removes the Jewel of Life from its staff before presenting Sheena with the empty staff. Sheena, unknowing of Marcus's true nature, goes off willingly with him to the temple.
Just in the nick of time, a Spiky-eared Pichu that Damos had previously befriended, through use of the same ability Sheena possesses, appears and gives him the jail cell's keys so they can escape.
At the temple, the eclipse begins and Arceus enters wondering why Damos isn't the one returning the Jewel of Life. Sheena tells Arceus that Damos is not coming as he planned to betray it. Arceus is shocked that his friend would ever turn against him, and Sheena attempts to give the Jewel to it, only for Marcus to initiate the attack. However this time the attack proceeds differently, as Marcus has altered the attack plan based on Sheena's information. This time, as well as attacking Arceus with the other controlled Pokémon, he begins to pour silver water onto Arceus which instantly hardens around it. Ash's group arrives and Sheena meets Damos for the first time, while Ash confronts the true villain. He and Dawn attempt to battle Heatran and Bronzong, but both are far too powerful. Instead, he attempts to defeat Marcus with hand-to-hand combat. This also fails, but Marcus drops the Jewel. It is nearly lost but Ash manages to recover it. Meanwhile, Damos and Sheena attempt to get to Arceus, however the two are almost killed by the silver water, but luckily Brock arrives and has Sudowoodo use Hammer Arm on the ground, creating a chasm for the water to fall into.
Arceus, meanwhile, is losing strength under the force of Marcus's attack, and without some of its Life Plates begins to die from the constant bombardment. Damos and Sheena combine their power and manage to touch the hearts of Damos' Pokémon, which are being controlled by the armor they wear. Ash and Dawn have Pikachu and Piplup destroy the armor on Heatran and Bronzong with Iron Tail andPeck. The assault frees them, and they turn on Marcus while the other Pokémon stop their attack. Marcus smugly declares that even if he fails, Arceus will still die, and the future that Ash and his friends came from will cease to exist, meaning they will no longer exist as well. True to his word, Pikachu soon vanishes, and Ash begins to vanish as well as he attempts to return the Jewel of Life to the nearly-dead Arceus. Damos manages to reach the last spark of life in Arceus' heart, giving it enough strength to reabsorb the Jewel and completely recover. With Marcus's plan thwarted, Pikachu is restored to life. As the area collapses, Arceus saves the group, as well as Damos' Pokémon, freeing the Pokémon in the process, then returns Ash's group to their proper time.
Arriving back in the present day, it appears that things have become peaceful due to the changes in the past. However, this is not the case - Arceus has completely defeated Dialga, Palkia and Giratina, and is preparing its final Judgment attack to destroy all of Michina Town. Ash cries out to it, begging it to remember that everything was fixed in the past, and just before the attack's destruction begins, Arceus remembers that this is true and halts its rampage. The changes to the past finally catch up to the present, restoring Michina Town to normal and healing the creation trio. Later, as the sun sets over Michina Town, the gang bid farewell to Dialga, Palkia and Giratina as they return of their own dimensions. Brock is confused as Michina Town is still flourishing despite the Jewel of Life being returned, but Arceus explains that Damos and the others devoted their entire lives to making sure Michina Town remained beautiful. Also, Sheena finds a new monument upon which there is an engraving of Ash, Dawn, Brock and Sheena as well as a message of thanks from Damos himself. Sheena begins to cry, now finally knowing the full truth about the ancestor she was ashamed of. Arceus says his goodbyes to everyone, but not before noting that for the first time it truly feels it belongs to the world they inhabit.
In the credits, it is revealed that Marcus went on to become an employee of Damos as a steward of the temple. In Alamos TownTonio and Alice fly in a hot air balloon while Baron Alberto attempts to follow them. Darkrai is then seen looking over the town. In a later scene, an imprisoned Zero is seen being visited by Newton Graceland and receiving a copy of Infi that survived the Megarig's wreck, much to his delight. Shaymin is also seen, looking out to a sunrise with a smile. Dialga, Palkia, Giratina, and Arceus are shown in their respective worlds, finally being able to live in peace once again.
Meanwhile, Team Rocket decide to steal some watermelons, only to come across a disguised Voltorb which sends them blasting off. Ash, Dawn and Brock continue their journey through Sinnoh, moving ever closer to their goals and with many more adventures still to come! Their Pokémon journey continues!


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