Molly's father goes to the desert in a small cave, with many hieroglyphics of Unown. He gets out his laptop, and starts taking pictures of each Unown that depict a letter. He then sees a block on the ground, which is a tile of an Unown. He picks it up and suddenly, the Unown appears right next to him, then disappears without a single notice. He finds a whole box full of the blocks, opens it up, and grabs some tiles. The Unown start to come to life, and they take him into some, other dimension. His assisstant notices that Molly's father is gone, right after his laptop drops on the ground, and only the box with the tiles remains.

Molly rushes down-stairs, in hope to greet her father, but to her disappointment, she only sees her dad's assisstant. She hears what has just happened, and starts to cry. Contemplating as she runs up the stairs, she takes her dad's computer into her room with the tiles, then looks at the pictures of Unown. She then opens the chest and starts to arrange the pieces, and eventually spells out "Mama, Papa, Me" with the pieces. A teardrop falls on them, while she wishes that her dad would come back. Suddenly, the pieces start to come arise, and crystals start to grow from where Molly is sitting. One of the servants hears something and tries to open the door. He does so until the crystals block the door, making it impossible to get in. They all flee from the house except for Molly because she is trapped. From the crystal, something starts to come into picture, which ends up being an Entei. She is confused at first, but then when she hears it speak, she asks who it is. Entei says that he is just who she wished for, her father. She realizes that her dad has come back, as Entei, while the whole area around the mansion becomes crystal.

All the while, Ash and his friends are trying to get to the next gym. They stumble across a female trainer, with an Aipom. Brock goes up to her, and complements her. Ash and the girl, whose name is Lisa, decide to have a battle.

Ash brings out a Totodile, while Lisa brings out a Granbull , which Totodile waterguns into a tree. Lisa brings out a Girafarig, while Ash brings out Chikorita. Chikorita uses Vine whip, while the Girafarig uses psychic, which hits Chikorita, making it faint. Ash takes out a Noctowl, and Lisa gets out her Aipom. Noctowl eventually dives, and hits Aipom, knocking it out. Ash takes out Bulbasaur to battle against a Butterfree, which Lisa brings out. Butterfree uses Sleep Powder, then Gust to knock Bulbasaur out. Ash then takes out a Cyndaquil, which Lisa retaliates with a Mankey, which Cyndaquil knocks out with a flamethrower after dodging a punch. For the final battle, it is Quagsire vs. Pikachu. Pikachu tries to shock it, but it is ammune to electric attacks. It hits Pikachu with a Water gun, but Pikachu recovers and jumps from a high tree branch to head butt Quagsire, knocking it out, and making Pikachu dizzy, but the winner none-the-less.

Ash, Misty, Brock, Lisa, and their Pokémon are all out, eating Lunch. Ash asks if there is a Pokémon Center nearby, and Lisa says that there is one in the Green Fields. Misty realizes that Green Fields is the number one spot for girls to go to, because of the beautiful flowers around the area. Of course, Brock wants to go, dreaming about all of the girls. After that, they go to Green Fields, but it is over-run by crystal. Nearby, Jessie and James are looking upon the area, and are not sure that they should have followed Ash.

The crystal seems to be spreading, going further and further away from the tower. Ash's mom is watching the area on TV. She runs to Professor Oak's house, and asks Tracey and Professor Oak if they are watching the news. They are too, and they all decide to go to Green Fields. Professor Oak and Ash's mom eventually meet up with Ash and the others, Ash hugs his mom, because he hasn't seen her in such a long time.

Molly is also watching the scene on TV, and she wishes that she had a mother. Entei rushes from the tower, going all the way to the Pokémon Center where Ash and the others are, and goes up to Ash's mom. Entei hypnotizes her into thinking that she is Molly's mom. Pikachu grabs onto Entei, but he gets Pikachu off. Entei goes back up into the crystal tower, and meets Molly, who thinks that Ash's mom is her mom, because she hasn't seen her in such a long time.

Ash and his gang are watching on as Professor Oak finds information on Entei. He finds out that the Unown's power is to read someone's soul, find out what they wish for most, and make it come true, so the Unown made Entei come into existence, because Entei had never been seen before. Another Pokémon trainer is watching the news, a female trainer that trains all Charizards. Ash's Charizard sees the news through a window, and decides to go help Ash get his mother back. He then starts to fly over to Green Fields. A bulldozer tries to take out the crystal that is surrounding the whole area where Molly is, but she gets mad that someone is trying to take her away. The Unown start making more crystal, destroying the bulldozer, and almost killing the person inside.

Ash's gang get an email, which they immediately open. It's from Molly, telling them to stay out, and not to interfere with her family. Of course, Ash decides to go save his mom, with Pikachu. Right before they get to the castle, Brock and Misty catch up with him, saying that they're going to go too. Then, Aipom comes up to them, and hands Ash a piece of Pokégear, which is a communicator. Lisa comes out, and wishes Ash a successful rescue. Ash, Misty, and Brock are all going through a tunnel made of crystal, walking through water, the only non-crystal part of the tunnel. Jessie and James are watching them going through the tunnel from their balloon, and decide to steal their Pokémon somewhere along the way. Entei notices the balloon, and jumps out to the roof of the tunnel, using an attack to create a large power sphere, and destroying the balloon. The balloon smashes through some of the crystal, and Jessie and James find themselves clinging to large pieces of crystal, which make up the tower, with a 100 foot-plus drop beneath them. When Ash and the others get to the end of the tunnel they call out Bulbasaur and Chikorita, who help them up onto a pathway above them.

Reporters are everywhere around the area and one of them finds Ash and starts interviewing. Molly sees what's happening on the TV, and so does Ash's mom, who snaps out of her trance, and realizes that Ash is her real child. Ash and the others get to the courtyard of the building, and see an entrance to the house. Unluckily, the entrance has been covered in crystal.

Ash calls out Cyndaquil, and tells him to blast through the door, but the crystal grows back. He tells him to try again, but not before Misty gets her water Pokémon out, too. Cyndaquil blasts through the door, then the water Pokémon shoot water around where Cyndaquil used his flamethrower. It kept the passageway open, and its large enough to put a human through. Pikachu goes through by jumping into the water stream, and gets blasted to the other side. The rest do this, until they get to Ash, the last one. He doesn't want to leave the Pokémon behind, so he grabs the water Pokémon, and jumps through, while they keep the hole open.

They run up the first flight of stairs, and enter a very strange area. Molly is watching this with Entei. He asks her if she wants to get rid of them, but she says that she wants to have a Pokémon battle. Unluckily, she doesn't have any Pokémon. Entei says not to worry, and he leaves the room, and flies away. An older Molly appears, about Brock's age, on his back. They get to a flowery field, around the same time Ash and the others do. Brock asks if she is Molly, and she tells them that she is. Ash and Misty look stunned, but Brock reminds them that anything can happen here. Brock decides to be in a Pokémon battle with her, while the other two go ahead.

Brock calls out Zubat, and Molly has a crystal Pokeball appear in her hand, which she throws out, with a Flaaffy inside. Zubat uses Confuse ray, then Wing attack, which both hit Flaaffy. It retaliates with a thundershock, which knocks out Zubat. Brock calls out his Vulpix, then Molly calls out Teddiursa, from another crystal Pokeball. Teddiursa uses Mega Punch, which nails Vulpix. Vulpix uses Quick attack, and Teddiursa uses Fury Swipes. Vulpix hits Teddiursa a couple of times, but Teddiursa eventually defeats Vulpix. In the background, Jessie and James are trying to sneak by Entei and the Pokémon battle. Vulpix is eventually knocked out.

Brock calls out Onix, so Molly calls out Phanpy. Phanpy uses his rolling tackle, which takes out Onix in one hit. While Ash keeps on going up the stairs, Ash's mom finds the book that Molly's dad used to read to her. She asks if Molly used to read this book, and she says that she used to, but Ash's mom can have it now, and she is so happy that her Mom and Dad are back. Ash gets to the top of the staircase, which is a flowery field, with the beach right next to it. 18 year old Molly appears there, on Entei. She says that she wants a better challenge, at that time, Misty challenges her to a battle. She tells her that she is a Gym leader, and Molly is surprised, because she thought that you had to be old to be a gym leader. Misty says that age nothing to do with skill, and a younger Molly appears, about Misty's age.

Misty says that she uses all Water Pokémon, so Molly says that she'll use water Pokémon as well. Molly raises her hands in the air and the ocean comes up, and engulfs them all. Ash tries to run up faster and faster, but the water keeps on filling up. It catches up to him, and he thinks that he's done-for, but when he breathes, its like breathing air. He remembers what Brock had said about anything can happen. He starts running up the stairs again. At this time, Molly brings out a Kingdra, and Misty brings out a Goldeen. As usual, Goldeen gets knocked out very quickly. Jessie and James are also here, and they start swimming up. Misty brings out Staryu, and Molly brings out a Mantine. The Mantine uses Whirlpool, leaving Staryu stunned, then uses bubblebeam, which almost knocks Staryu out, but Staryu uses recover, then tackle. Molly enjoys her battle saying how exciting it is.

As Ash goes up the final set of stairs, he goes up to his mom, who is with Molly, sleeping on her lap. Ash's mom tells him that Entei just left, and Ash explains the whole story to her. Ash's mom wakes up Molly, and tells her that Ash is her child, not Molly. Molly doesn't want her mom to leave again, and she starts to cry. Crystal starts to burst out all around her. Entei notices what's happening, and comes back up. He protests, saying that Ash's mom is not Molly's mom. Ash brings out Totodile to fight against Entei. Totodile tries water gun, but Entei retaliates with his mouth beam, which immediately knocks out Totodile. Cyndaquil gets called out next, and he tries to use flamethrower on Entei, but Entei uses his mouth beam again. The two attacks start in the middle, and start to go towards Cyndaquil, and eventually knock him out.

Ash tells Entei that he's a legend, not Molly's father, which causes Molly to cry, and crystal to go everywhere. Entei tells him that he is the father, and then attacks Pikachu with his mouth beam, after Pikachu attacks with his Thundershock attack. Right as the two beams hit, Jessie and James come in, thankful that they're safe now, but when the two beams hit, they start to have second thoughts. Entei attacks Pikachu again, but Ash gets in the way, and pulls Pikachu away. Unluckily, this beam hit near a wall, and the wall where Ash and Pikachu collapses. Thankfully, a Charizard saves Ash, before it hits the ground. Ash recognizes this Charizard's behavior and realizes that the Charizard is his Charizard. A large battle starts with Ash on Charizard. The battle lasts a while, and it ends with Charizard under Entei's foot and Entei ready to destroy Charizard. Right before Entei takes Charizard out for good, Molly pleads for her father not to harm Charizard. Misty and Brock both tell Molly to go with Ash's mom, and also kiss-up by telling her that she's really good at Pokémon battles(which she is). Ash's mom puts her hand out, and Molly holds it, and they both hug. Molly cries in joy, and the crystal starts to go away. Entei starts to leave, saying that if she is happy like this, he is happy as well.

They try to leave, but the Unown realize what is happening, and they don't want Molly to leave, so they start to make crystal all around. Entei blasts through it, and they all start to make a run for it down the stairs. While this is happening, the crystal's growth starts to get out of control, and it starts to engulf the Pokémon Center. Ash and the others find all of the Unown blocking the way out. Ash tries to run through, but an invisible wall makes him fall back. Charizard tries to go through, but the same thing happens. Charizard tries to blast his way through, but the wall just patches itself back up. Pikachu uses thunder, and it creates a hole, but it too is quickly patched up. The Unown start to get mad, and they make crystal go all over, almost impaling Ash, and some of the others. Entei comes through a wall, and decides to help Ash and the others. He destroys some of the crystal, and tells them that he was happy that he was Molly's dad, but he is still just as happy helping her instead.

Entei tries to use his mouth beam against the Unown, but nothing happens. He charges the field, and stays there, slowly destroying it. Charizard and Pikachu help too, using flamethrower, and thunder again. Molly tells her dad to keep on trying, and with the words of encouragement, they all break through. Entei leaves, and goes into Molly's dreams again. Some of the Unown turn into tiles, and they all go into a portal. The crystal starts to disappear, and the beautiful Green Fields are made visible again. They all leave, and Molly sees a cloud that looks like Entei, and smiles. Many police start to come, so Jessie and James figure that they're stuck in the house. Molly's dad is also returned from the tiles, and starts to make his way home. Within the credits, Molly's dad comes back with her mom with him. It also shows Molly hugging them both in her happiness.