One day, while exploring the forest Yuna and her fiends discover a red dragon named: Latias and befriends them but then Latios her older brother: Latios. At first he doesn't trust them, now he does later. But an evil hunter named: Sideshow Bob and his R2 unit: R2-Q5 are hunting them both to be powerful on earth. Can Yuna and her friends defend Latios & Latias?
Story of Latios and Latias/The present
Long ago, there was a forest home of Pokemon and their guardians were Latios and Latias. The 2 were then chased by a Pokemon hunter when a colt, named "Isamu" who entered the forest had saved them and they went back in time. Then in the present year, we see Sideshow Bob talking to the same hunter who haunted them 4 years ago, when he refused. His droid, "R2-Q5" releases a Tyranitar. And Sideshow Bob catches it with a Dark Ball that turns it evil, and orders it to destroy the hunters home till the hunter tells Sideshow Bob where he found them.
With Yuna and the gang
Meanwhile, Yuna, her friends, and their dragons are in the forest till they are stopped by park ranger, Homer Simpson. He then explains that their dragons could cause trouble, and they meet his wife and his dad in a cottage. In the cottage, they explain about the time travels in the forest. And then they wander through the forest. They witness a glow and there was Isamu the colt brought back from time. Then 2 giant Pokemon then leave the colt and go into the woods.
At the cottage/Isamu awakens
Yuna and her friends then take Isamu back to the cottage. He then awakens, he was then shocked to see the new faces around him. And shoves Yuna and the 2 get into a quarrel until Nightstar breaks it up. And Marge arrives and explains he's the lost colt, who disappeared 4 years ago. Marge then gives the colt his sketchbook back. Marge then explains about the 2 Pokemon from before, and Yuna says they can find them.
Finding Latios and Latias
In the woods, Nightstar senses something. And then they come to a big tree and see Latias! But find she's partly injured, before they get closer Latios unexpectedly attacks them. But after some reasoning, they manage to befriend Latias. But Latios still doesn't trust them.
Encounter with Sideshow Bob and R2-Q5
As they race for the healing springs, Sideshow Bob and R2-Q5 show up! The 2 then try to capture Latias, by using the Tyranitar. But Crystal Heart and Eclipse use their smoke to escape. And soon, Bob sets out his Scizor and Weaville. But as they continue, Nyx twists her left front knee and then soon enough, Scizor and Weavile attack them. But Eaglesight and Singun battle them and Isamu has his own dragon, Gray and they defeat the 2 evil Pokemon.
Arriving at the Healing Springs
In the fog, they've encounter a Ursaring. And they follow it through the forest and there was the Healing Spring! Isamu then guides Latias into the water and she is healed. And Latios then trusts Yuna and the gang Then they all join them for a swim and Nyx's knee is healed at the same time. Then they arrive at a tree with delicious berries. As they eat some, Sideshow Bob and R2-Q5 continue to search for them.
That night/Isamu's story
That night, while some of our heroes are asleep, Isamu is sketching Latias, Latios, and Nightstar when Yuna notices him he asked him why was he out in a forest. Isamu then explains that his mother was a dragon breeder and he ran away from because he felt like he couldn't be as good as his mother. Yuna was shocked to hear this and tells Isamu that he should be like an adopted brother. This then made Isamu feel a little better. Then the 2 Pokemon wake up. Which also wakes up Nightstar. And then they see some lights in the forest. And there was Butterfrees! Then they climbed up a tree and watched them fly off as the sun began to rise.
Latios captured!/The Evil Latios
Then as the group go through the woods again, they are encountered by Sideshow Bob and R2-Q5 again! This time with claws, the dragons try to get rid of them, but R2-Q5 cuts down trees and then grabs Latios! Sideshow Bob shocks him, lifts him in the air, and catches him with a Dark Ball. And Yuna fights Sideshow Bob, and soon he then crushes her hove and Pokemon surround him. And sends out Latios comes out but this time, he's evil! And then he tears apart some of the vegetation and creates a giant sphere around himself. Homer, Marge, and his dad see this and set off. And high above the forest, Rayquaza (whom Skyla saw him earlier in the beginning) flies down.
Latios' creation/Rayqauza saves Yuna, Nightstar, and Isamu
As Latios continues on, the creation then transforms into a monster. And then it starts to destroy all the trees! The team then flies after the monster in and call for Latios. But Sideshow has Latios shoot them down and destroys the spring. Isamu and Yuna, riding Nightstar, then prepare to free Latios and battle Sideshow Bob but then the monster prepares to blast them when Rayquaza came out of the sky and saves them, and Latios squeals for Rayquaza's help to save his brother and the legendary Pokemon agrees. But then Sideshow Bob releases his his Tyranitar. But then Stovestomach battles the Tyranitar while Rayquaza gets Yuna, Isamu, and Nightstar closer to Latios. But Latios shakes them off. And then starts shocking them, Tyranitar and Stovestomach keep battling. And soon enough, Stovestomach throws Tyranitar into the spring. Bob orders Latios to get Rayqauza, and he shocks Rayquaza as Yuna, Isamu, Latias, and Nightstar get in the monsters mouth. They all then try to snap Latios out of the evil control. Then, Latios completely remembers and Bob's Dark Ball that controlled Latios is destroyed. And his creation collapses into the spring waters.
Latios dies and resurrection/Sideshow Bob and R2-Q5's defeat
They then all swim to the shoreline but Latios is very weak and then he then collapses. Realizing he's close to death they try to heal him in the spring waters but the water is tainted. Sharon then arrives and cleans the water. But when they place Latios into it, it still wasn't working. They still try to get Latios to wake up but they all started to cry, Latias comes to her dead brother and lays besides him, angry and upset. But then something glows from the sky then a bunch of Latios and Latias came down and lifted Latios, and Latias followed them. Then as they surround him, Latios then emerges alive and well! And once all the Latios and Latias leave, Latias and Latios played again. But then Sideshow Bob and R2-Q5 grab them! Bob, holds out a gun. And the 2 villains fly off, but Latios and Latias break free and they both start to battle Bob and R2 and destroy their jetpacks and both fall and land in the branches. While the 2 Pokemon fly back down, the Pokemon tie up Bob and his droid unit. And then Rayqauza leaves.
Latios and Latias' depart
Just then a portal opens up in the sky and Latios and Latias request Isamu to join them, Isamu then gives the team a last goodbye (Yuna and Isamu then share one last hug and Nightstar nuzzles him). And the 2 Pokemon and Isamu depart. At Canterlot, the group share about their adventure and Luna sees Yuna looking very sad. Yuna then explains about Isamu. But Luna assures her that Isamu will return someday. In the forest Sideshow Bob and R2 cut themselves free but decided to get a different job.
- Homer Simpson, Sideshow Bob, and R2-Q5 guest star in this film.
- The film marks it's first appearances of Latios & Latias.
- This film has a "Pokemon 4Ever" mix in it.
- Legend/Altomare (from Pokemon Heroes) "The story of Latios & Latias"
- "Celebi Revived" [when the other Latios and Latias show up]
- There's a Place For Us (end song)
- Story of Latios and Latias/The present
- With Yuna and the gang
- At the cottage/Isamu awakens
- Finding Latios and Latias
- Encounter with Sideshow Bob and R2-Q5
- Arriving at the Healing Springs
- That night/Isamu's story
- Latios captured!/The Evil Latios
- Latios' creation/Rayqauza saves Yuna, Nightstar, and Isamu
- Latios dies and resurrection/Sideshow Bob and R2-Q5's defeat
- Latios and Latias' depart