NOTE: This spoiler was submitted by Mark I who says, "This movie takes place in an alternate continuity to the TV show, and is a retelling of Ash's first journey through Kanto."
The movie begins in a stadium where a Pokémon battle is proceeding between two trainers (in one of many easter eggs, the two trainers previous appeared in Mewtwo Strikes Back, the very first Pokémon movie). Watching it on TV is Ash, a boy from Pallet Town in the Kanto region, who will be setting off on his Pokémon journey the next day and choosing his first Pokémon from the standard selection of Bulbasaur, Charmander, and Squirtle. However, he is so excited that during the night, he dreams he is a trainer and accidentally throws his Poké Ball-shaped alarm clock, breaking it. The next morning, Ash's mom Delia wakes her son telling him he overslept. Panicking, he runs to the laboratory of the town's Pokémon expert Professor Oak who realizes Ash is the fourth (and last) beginning trainer he's expecting that day. Unfortunately, the three starter Pokémon have already been claimed by trainers who were on time. A desperate Ash is willing to take any Pokémon available at this point, and Professor Oak tells him there is one more Pokémon available; a troublesome yellow Pokémon known as Pikachu. Ash declares Pikachu to be the best of all and accepts, happy he's getting a Pokémon at all. Unfortunately, Pikachu is an electric-type Pokémon and enjoys electrocuting Ash (whom it doesn't like very. Professor Oak gives Ash Pikachu's Poké ball; however, Pikachu steadfastly refuses to get inside as it doesn't like being confined.
Ash sets off on his journey dragging an uncooperative Pikachu behind him on a leash but eventually takes it off as a sign of good will. Ash sees a Pidgey nearby and tries to capture it by throwing a Poké Ball, but it gets out. Remembering Pokémon have to be weakened before they can be captured, Ash tries to send Pikachu to take it on, but Pikachu refuses. Ash is then forced to try throwing rocks, but accidentally misses Pidgey and hits a Spearow instead. Spearow is very angry but takes its anger out on Pikachu who fights back with its electricity and sends it into a tree where it reemerges with its entire flock, dozens of Spearow which chase Ash and Pikachu whom they manage to severely injure when they catch up and start attacking it en masse. Ash picks up Pikachu and tries to lose the Spearow by jumping into a fast-moving river (nearly getting eaten by a Gyarados for its troubles) but still can't shake it. As he's running, a heavy rainstorm begins, and Ash ends up slipping in the mud. Ash promises Pikachu he'll protect it and asks that it get inside its Poké Ball where it'll be safe. Deciding to stop running away, Ash then stands up to the Spearow flocking vowing that one day he'll be a Pokémon Master and will catch all of them. The Spearow fly at Ash, but Pikachu jumps off Ash's shoulder and lets out a massive Thunderbolt which sends the Spearow flying away. As they recover, the sun emerges and a rainbow forms. Ash and Pikachu then see a magnificent flying Pokémon flying by into the rainbow, during which is drops a feather which is picked up by Ash who vows to Pikachu that one day they'll get to meet the Pokémon they just encountered. Pikachu agrees, and a friendship is born.
As the theme song plays (a remix of the original series song), Ash and Pikachu begin their journey together. They win battles, strengthen their bond and manage to make their first capture, a Caterpie. Ash also begins challenging the Pokémon Gyms and defeats Erika, the Celadon City Gym Leader, for the Rainbow Badge (his third). At this point, Ash decides to go to the local Pokémon Center and call his mom and let her know how he's doing. Delia is furious as she hasn't heard from him for a while despite leaving messages all over asking him to phone. Ash apologizes but then overhears that an Entei (one of the Legendary Pokémon) has been spotted close by. Ash quickly hangs up and goes chasing it, as does everyone else in the place (which includes Jessie, James, and Meowth of the villainous Team Rocket).
Ash quickly finds Entei nearby and sends Pikachu to battle it, and as he does a girl named Verity appears and sends her Pokémon, Piplup out to battle it too. However, neither Pokémon makes much on an impact on Entei, who seems to take a special interest in Ash. At the same time, another boy called Sorrel arrives and tries to battle Entei with Lucario, but it eventually beats them all and runs off. Ash and Verity blame each other for what happened and decide to battle each other however Sorrel warns them a rainstorm is coming. The two don't believe him and battle anyway with Pikachu and Piplup, however, during the battle, they accidentally strike an Onix which is furious and attacks. Ash, Verity, Pikachu, and Piplup try to run away from the gigantic rock snake, but accidentally end up on its back. As it tries to shake them off, Ash jumps off and in front of Onix, blocking the way. Onix is ready to crush Ash, however, Piplup protects Ash with a Whirlpool attack, allowing Ash to apologize. Onix accepts this and burrows away. Ash and Verity apologize to each other, just as the predicted rain starts. Meanwhile, Team Rocket decide to try and capture Entei but get blasted off into the sky for their trouble.
The two look for shelter when they see a Charmander on a rock. The two approach it as it seems to be waiting for someone. Suddenly a boy named Cross appears with his Dusk Form Lycanroc, and Charmander happily runs towards him. Cross, however, kicks Charmander away, disgusted that Charmander would have waited this long for him to return. Ash and Verity are disgusted, but Cross doesn't care tells them that strength is all that matters when it comes to Pokémon before leaving. The rain is now falling heavily, and Charmander's tail flame is nearly out leaving it close to death. The two run with Charmander to the nearest shelter, a large cave where Sorrel is also residing. Upon seeing Charmander's condition, Sorrel, who wants to be a Pokémon Professor so has some knowledge of Pokémon medical training, treats it and leaves it to recover overnight next to a fire. The three then introduce themselves to each other, with Sorrel explaining that he wants to learn about Legendary Pokémon to help with his dream when Entei walks in with other Pokémon looking to escape the bad weather. They decide not to disturb it and at the same time Marshadow, a Mythical Pokémon, takes interest in Ash and hides in his shadow. Verity and Sorrel recall Piplup and Lucario into their Poké Balls to protect them from the cold, but Pikachu again refuses to get into his. Piplup and Lucario then emerge from theirs, and their trainers decide to let them stay outside. The next morning, Charmander has completely recovered, and Ash asks it if it would like to go with him. Charmander agrees, and Ash captures it. Ash, Verity, and Sorrel (who are both from the Sinnoh region) decide to travel together for a while.
The three have many adventures, and one day Ash sends Caterpie out to battle a Pinsir causing it to evolve into Metapod. Pinsir gets away, but Ash is happy enough that Metapod evolved. That evening, Verity looks through pictures on her phone (which reveal that her mother is none other than Sinnoh League Champion Cynthia) when she hears a noise and spots Suicune looking at her. Verity tells the others what she saw, and also admits she traveled from Sinnoh to Kanto to get away from her overbearing mother. Later at the Pokémon Center Sorrel looks up the legend of Ho-oh and how it revived three Pokémon who died in a fire to become Entei, Raikou, and Suicune. Ash recognizes Ho-oh as the Pokémon he saw after the incident with the Spearow and shows Verity and Sorrel the Rainbow Wing which shoots a beam of light into the distance. Sorrel looks up information and finds that Ho-oh is looking for a RainBow Hero to fight for it, and warns that Rainbow Wings lose their color if in the hands of an impure person. They find that the beam of light headed towards a nearby mountain range, so the three decide to go there and meet Ho-oh. On their travels, they meet Bonji who tells Ash it may be his destiny to meet Ho-oh. That night, Sorrel tells a tragic story from his past; his family owned a Luxray which was a very good friend to him. One night, he got lost and injured in a snowstorm and was lying helpless when Luxray found him and curled up around him to keep his body warn in the cold weather. Although Sorrel survived, Luxray froze to death and following that Sorrel found it hard to trust Pokémon since he knew they would eventually have to leave him. Sometime later, Ash uses Charmander to battle a lady's Jigglypuff. Charmander wins and evolves into a Charmeleon.
Sometime later, Ash is battling a trainer's Snorlax with Pikachu who manages to win using an Iron Tail/Thunderbolt combo. Ash is ready to take on another challenger when none other than Cross arrives. Determined to show the arrogant trainer a thing or two, Ash uses Charmeleon in the battle against Cross' strongest Pokémon, Incineroar. Charmeleon starts off strong and hits Incineroar with powerful attacks; however, Incineroar simply absorbs them then uses the energy to fight back and manages to completely thrash Charmeleon. Ash tells Charmeleon to fight back, but Charmeleon is out of energy and can't produce its fire. Ash doesn't notice his Pokémon is struggling badly and wants to continue the battle, and as a result, Charmelon is badly injured by Incineroar. Cross gives Ash a verbal beatdown, telling him he's the worst trainer he's ever faced, and raw strength is all that matters when it comes to Pokémon. Ash takes Charmeleon to a Pokémon Center where it is healed, but Cross' words are still ringing in his ears, and he tells the others that if he'd battled with Pikachu instead of Charmeleon, then he would have won the battle. Verity and Sorrel are shocked, warning Ash that Charmeleon would be hurt if it heard those words, but Ash doesn't care and runs away into a forest trying to lose them. Pikachu follows but Ash just wants to be left alone and, in the heat of the moment, says that he wishes he'd been able to start his journey with Squirtle as he'd planned. Pikachu is hurt by these words, and when Ash turns around Pikachu is gone while the Rainbow Wing starts to darken in response to the severe change of attitude. Marshadow emerges from Ash's shadow and hypnotizes him, causing the young trainer to fall asleep and dream...
Ash wakes up at home on the morning he began his Pokémon journey, except he's living in a world where Pokémon don't exist and he's late for school this time. He heads there (where he is once again behind everyone else) and finds himself in class with Verity and Sorrel. During the day he sees Pikachu's essence running about but can't remember what it is. Later, he looks into the distance and tells Verity and Sorrel that he'd like to go on a journey and see the world. Just then Verity and Sorrel vanish, and Ash sees Pikachu's essence and runs after it desperately to catch it only to find himself falling. Ash wakes up back in the forest and finds Pikachu in front of him with Sorrel and Verity who have been searching for him for hours. Ash apologizes to Pikachu and Charmeleon (through his Poké Ball) for what he said, and the friends all make up as the Rainbow Wing returns to its usual colors. Pikachu then spots Marshadow's eyes watching and tries to use Thunderbolt on it, but the tree Ash is lying against conducts the electricity and sends it throughout the forest causing many angry Primeape to fall from the trees and attack. Everyone tries to run, but the Primeape catch up and start throwing everyone into the air. Verity warns Ash that directly attacking the Primeape will make them angrier and more powerful to Ash sends out Metapod and ties them up with String Shot. They then run away, and during the escape, Metapod evolves into Butterfree. Meanwhile, Team Rocket run into the Primeape and are thrown into the air instead (seriously, their whole role in this movie is just encountering the Pokémon Ash has and getting blasted off... he never even knows anyone is following him).
Emerging from the forest, the gang see a Pink Butterfree being attacked by a Fearow. Ash uses his Butterfree to save it, and both Butterfree are taken with each other. Following them, Ash and the others see Raikou briefly then emerge onto a cliff where they spot hundreds of Butterfree preparing to head south to spawn. Ash's Butterfree and the Pink Butterfree do a courtship dance, and Ash is delighted the two have decided to get together until he realizes that if he lets Butterfree proceed with its mate, he'll never see it again. Despite wanting Butterfree to stay with him badly, Ash decides letting it go is the right thing to go. He does so, and tries (in vain) to fight back tears as he sees his friend leave.
The three trainers reach the mountain range where Ho-oh live, and the Rainbow Wing points Ash towards Mt. Tengan, the highest point where Ho-oh is known to visit. As they near the top, Bonji appears again and tells Ash that a rainbow flower is blooming (in reality, a rock is glowing with the colors of a rainbow) and if he touches the flower with the wing then Ho-oh is certain to appear. Bonji then tells them that Marshadow usually accompanies, judges and guides trainers who are wanting to meet Ho-oh. What no-one realizes is that Cross has heard everything, and he makes an attempt to steal the Rainbow Wing from Ash, telling him that he also saw Ho-oh when he started his journey but he wasn't left with a Rainbow Wing and doesn't understand how he isn't worthy to meet it. Cross sends out Incineroar, and Ash sends out Charmeleon for a rematch. This time, Charmeleon is a lot stronger and during the match evolves into Charizard. Using its new power and ability to fly, Charizard manages to soundly defeat Incineroar. Ash tells Cross that he isn't on his journey just to become more powerful but also wants to make new friends. This just further angers Cross, who tussles with Ash and steals the Rainbow Wing as he declares he intends to crush Ho-oh. However Cross fails to notice the Rainbow Wing darkening in his hand, and when he touches the flower with it, the rock also turns black and sends out dark energy. Marshadow picks up the darkened Rainbow Wing and is furious this was allowed to happen and attacks the trainers by taking control of all the nearby wild Pokémon as well as Cross' Lycanroc.
Ash tries to stop Marshadow and approaches it, covered by Verity, Sorrel, and Cross. Ash battles Marshadow with Pikachu while Charizard and the other trainers Pokémon battle the ones under Marshadow's control. Cross tries to protect Ash from Lycanroc (with Charizard protecting Cross, showing it still had some loyalty towards its former trainer) and is bitten on the arm for his trouble; however Cross reminds Lycanroc this happened on the day they met, which helps snap Lycanroc out of its trance. Pikachu battles Marshadow hard, but is unable to defeat it and is wounded in the process. The wild Pokémon try to attack Pikachu as it lies helpless, but Ash shields it with his body and is also hurt. As the Rainbow Wing disintegrates and the Pokémon prepare to attack again, Ash lies next to Pikachu and asks it to get into its Poké Ball. Pikachu refuses, and Ash asks it why it never wants to go inside... and Pikachu answers (as in, actually SPEAKS ENGLISH!) that it won't go inside as it wants to stay at Ash's side forever. Ash stands up and protects Pikachu, just like he did against the Spearow, and when the Pokémon fire their attacks Pikachu tries to jump off Ash's shoulder again as it did before... but this time, it stumbles and falls. A weakened Ash catches Pikachu and finally manages to return it to its Poké Ball just before he takes the full force of the attack. Pikachu instantly comes back outside the Poké Ball and sees Ash lying dead and fading away. Pikachu and the other trainers watch devastated as Ash's body disappears.
Ash wakes up where he fell but finds no-one around (he is now in some form of afterlife) and calls out for Pikachu. Suddenly a tunnel appears, and Ash starts to run through it, as in the real world a portal appears in front of Pikachu from which Ash's voice emerges. Ash runs through the portal which turns rainbow colored (its implied that Ho-oh is restoring Ash to life as it did the Legendary Beasts) as Pikachu jumps through. Ash and Pikachu are reunited and emerge back into the real world, and Marshadow forgets its anger as the Rainbow Wing is restored in Ash's hand. The rainbow flower blooms again and this time Ash, now unhindered by Cross, succeeds in touching the flower with the wing. Ho-oh appears and flies over the mountain, and Ash challenges it to a battle. Ho-oh accepts, and it begins to battle Pikachu. Obviously, Pikachu loses but Ash doesn't mind; he's just happy to have met Ho-oh properly. The gang bid farewell to Bonji who looks forward to the day he can see Ho-oh again.
Ash makes amends with Cross, and the two (now friendly) rivals agree to battle again someday. He then parts ways with Verity and Sorrel, as Verity decides to head home and visit her mom and Sorrel wants to investigate the Legendary Birds (Articuno, Zapdos, and Moltres). Moving on, Ash and Pikachu continue their Pokémon journey, as scenes from Johto, Hoenn, Sinnoh, Unova, Kalos, and Alola play on screen and the narrator promises that the two have many more adventures to come.
Over the closing credits, images are shown of all of Ash's traveling companions from the TV series. Ash is then seen preparing to battle a Heracross, as Verity travels on a ship bound for Sinnoh and Sorrel manages to see Articuno.
*CUT TO THE CHASE*
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Ash and his friends make it to Mt. Tengan to summon Ho-oh, but his rival Cross steals the Rainbow Wing and tries to do so instead. Since his heart isn't pure, this instead causes Marshadow to take control of all the wild Pokémon and attack. Ash dies protecting Pikachu from the wild Pokémon but is revived by Ho-oh. Ash then has his long-awaited battle against Ho-oh but loses. He then bids farewell to Verity and Sorrel and continues his Pokémon journey.
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