The movie starts with Brock giving a summary about what pokemon is about.

A girl then starts to look in a book about Latios and Latias. She is talking to another person. A security guard then comes and the two girls hide. The security guard then sees a rose sticking out of one of the books. The girls then slide down a wire to the to the other side. The girls get into their car and drive off. One of the girls is named Oakley. They both work for Team Rocket. They drive off a cliff and then start to fly. They then start to talk about the Soul Dew. They then head for the city of Altomare.

Ash and Misty are in the water pokemon competition. In this competition, people ride rafts while their water pokemon pull them. The first person to cross the finish line wins. The announcer then talks and the Xatu rings. Everyone takes off and Brock talks to a girl in the audience. Everyone seems to be doing very well in the race. A Latios and Latias then start to fly around but they�re invisible. They both watch the battle. Team Rocket is eating but they get sprayed by water and their food gets soaked. Brock then starts to talk to the same girl but an old woman appears instead. Ash falls in the water and they get back up. However, Latios is pulling Ash along. Misty and another person is in the lead but Ash catches up. However, they go the wrong way and they lose the race. Misty and the another person comes in but Misty wins.

The person that lost to Misty offers to give her a tour around Altomare. Ash�s Totodile feels sad but then it cheers up. Latias and Latios then fly off. The person (his name is Ross) gives them a tour in a boat. Misty then gets a jewel sort of thing. Ross then tells them about the guardians of Altomare. These guardians are Latias and Latios.

A walking camera then comes in and it starts to video tape the townspeople. The owner of the camera are the two girls (there names are Annie and Oakley) who plan to capture Latias and Latios. They explain that they can take the shape of humans. The scanner then finds one of them.

They go on a boat and Jessie, James, and Meowth get splashed. They then start to follow them.

Ross continues the tour and finishes it. They plan on going to the ice cream place. Pikachu sees a girl and her Vaporeon. The same girl lets Pikachu drink some water. Ash then comes and the girls looks at Ash very closely. The girl then runs off.

Annie and Oakley spy on the same girl that Ash met because they know that the girl is really Latias in disguise. They pull up towards Latias and they talk to it. Annie and Oakley send out Espeon and Ariados and the two pokemon start to chase Latias. Pikachu then runs away and Ash follows it. Ariados blocks Latias�s path and Espeon freezes Latias while Ariados uses a String Shot on it. Annie and Oakley head up and Ash and Pikachu come. Ash gets Latias free from the webs and Espeon fires a ray at Ash. Pikachu then uses Thunderbolt and Annie falls in the water. Espeon and Ariados then go after Ash.

They start to have a chase around some buildings. Latias then leads Ash up some stairs and up to safety. Misty and Brock then talks to Ash. Ash realizes that he is back where he�s started and he notices that Latias has disappeared.

Ash and the others then get together again and they are at the museum. The same camera that Annie and Oakley use is scanning the town. They see the kids.

Inside the museum, they see some fossils. A man (Lorenzo) comes and explains to them that the fossils once terrorized Altomare. The fossils are Aerodactyl and Kabutops. Lorenzo shows them around the museum. Lorenzo then tells them about the history of Altomare.

Ash then sees the same girl that he met before. The girl leads and Ash heads off to chase after the girl. Ash sees the girl walking on the sidewalk but the girl is just too fast for Ash. Ash goes across the bridge and the camera starts to spy on them. The girl then says that she doesn�t know Ash and walks off. A bunch of Murkrow squawk and Ash sees the girl again. It seems that the girl is leading Ash to a certain place.

Ash then sees a forest-like pace. The girl then goes right through the wall and so does Pikachu. Ash then does it too. Ash walks in the dark and then light comes. Ash sees a whole new place with lots of pokemon in it. Ash then sees the same girl and she is swinging on a swing.

Suddenly, an invisible pokemon splashes out of the water and sprays Ash and Pikachu. This pokemon is Latios. Latios flies around. PIkachu�s Thunderbolt misses Latios and the girl blocks Latios from attacking Ash. Ash then realizes that the pokemon is Latios.

A girl wearing a hat and carrying a book comes out and asks why Ash is here. This girl looks exactly like the one who brought Ash here. Lorenzo from the museum comes and tells Bianca that Ash meant to harm. The girl then comes and puts Ash on a swing. The girl then reveals herself as Latias. Latios then licks Pikachu on the face. Pikachu then flies with Latios and Latias. Bianca apologizes and Bianca explains why Latias looked like her. Latias then takes Ash�s hat but then he gets it back.

Latios and Latias�s eyes start to glow and Latios dives into the water. Everyone then transforms into a different place. The old man calls it �sitesharing� and that they are seeing exactly what Latios is seeing. Latios swims through many pokemon and then the �sitesharing� ends.

Lorenzo then tells Ash that he�s known Latios and Latias since they were babies and that they brought water to their town. They then talk about the Soul Dew and that the other Latios died from saving the town. Ash then sees some diagrams that shows people how to power the Soul Dew. Lorenzo then takes them to where the Soul Dew is held. It�s held in a pool of water.

Latias then picks up Ash and drops him but Latios catches him. Lorenzo, Ash, and Veonca go back. The camera then sees Latias and Latios. Then the three of them visit the old man�s workshop.

They go back outside and Veonca and Ash leads them back on a boat. On the boat ride Ash tells Veonca that two girls were chasing Latias.

Annie and Oakley then hop on roofs and Jessie, James, and Meowth follow them. Jessie, James, and Meowth land on a pole and because of Wobbuffet, they fall down.

At Lorenzo�s workshop, Espeon comes in and uses Hypnosis to put Lorenzo asleep. Latios and Latias then wakes up. Annie, Oakley, Espeon, and Ariados comes in. Latios then starts to attack them. They dodge Latios�s attack, but then Latios and Latias become invisible. Annie and Oakley then put on some special glasses in order to see the two pokemon � even if they are invisible. Espeon then uses its Swift attack and Ariados uses Night Shade which Latios blocks. However, Oakley throws something which captures Latios and zaps it. Espeon then uses Psybeam which takes down Latias. Espeon then uses Tackle but Latios blocks it. Espeon and Ariados continue to hurt Latios more with Psychic and String Shot attacks. Latias dives into the water and escapes.

With Latios captured and Latias gone, Oakley takes the Soul Dew but it�s stuck. With a few good yanks the Soul Dew comes off and they both examine it. Oakley then finds the diagrams of how the Soul Dew works.

Latias comes out of the water. Lorenzo and Bianca then realize that the Soul Dew is gone. They then decide to head for the museum.

Inside the museum, Annie and Oakley carry Latios back. Latios is then put in the middle of a circle and a machine activates. Then the old man and Veonca come but Espeon uses Psychic attack on them. Oakley then puts the Soul Dew in the machine and the machine starts to move.

Latias comes to where Ash and the others are sleeping. Pikachu wakes up and Latias enters the room as a girl. Ash then tells Misty and Brock that the girl is Latias. Latias then changes back to a pokemon.

Back in the museum, Lorenzo and Bianca get tied up. Latios opens its eyes. Oakley goes inside the control center. Latios�s eyes start to glow and so does Latias�s. They then do �sitesharing.� They see that the Soul Dew was stolen. Oakley goes inside the control center and she brings back Kabutops and Aerodactyl. Oakley then tells the two fossil pokemon to get Latias. The �sitesharing� then comes to an end and they are transferred back to the room.

Jessie, James, and Meowth walk along the sidewalk. They see an exit but Oakley blocks it off. They are trapped. Oakley then starts to block off a lot of doors and entrances. Ash and Latias jump from a ledge and falls into the water. Ash then decides to go to the museum. Ash finds a boat and they head off to the museum.

In the museum, Oakley continues to run the machine.

Meanwhile, Latias continues to pull Ash on the boat. Aerodactyl then comes from behind Ash and swoops down and grabs Latias. Ash jumps onto Latias and Pikachu uses Thunderbolt, which frees Latias. Latias falls into the water but gets back up and turns invisible. Aerodactyl then uses a Hyper Beam which destroys the boat. Ash sinks to the bottom of the sea but Latias carries Ash back up to the surface. Pikachu swims safely to Ash.

Then Ash sees the same rafts that he used in the race at the beginning of the movie. He takes one and Latias pulls him. Aerodactyl follows them but Ash loses it.

Misty and Brock tries to get through the gate, but it�s locked. Misty and Brock sends out Crobat, Corsola, and Politoed to help Ash. They then dive into the water. Brock also climbs the gate.

Kabutops comes and tries to get Ash but Crobat, Corsola, and Politoed defeat Kabutops and they save Ash.

The machine is still on in the museum and Oakley sees Latias and Ash through the screen. Oakley then creates a tidal wave.

The tidal wave forms and is headed for the town. The wave then comes crashing down and Ash is trapped in the middle of it. Oakley does a few things with the wave and Ash can�t hold his breath for much longer. Latias then frees them from the wave and the wave disappears.

Back at the museum, everything is starting to go out of control. Ash and Latias arrive at the museum and Pikachu Thundershocks Annie. Pikachu then shock the ropes to free Bianca and Lorenzo. The machine is still out of control. Latias is trying to break through the sphere in which Latios is in. Ash tries to break through but has no success. They then try to pull Latios out and they succeed. The machine then stops.

Annie comes to rescue Oakley. Brock and Misty come too. Annie then sees that the Soul Dew is black and red. Annie reaches out for it and Lorenzo tells her not to touch it. Annie touches it anyways and a light bursts from it. The Soul Dew is dying and all the water is leaving.

Latias and Latios fly above in the sky and the water comes and destroys a lot of the town. Latias and Latios then fly into the water and they start to glow. The water returns to its normal self. Latias looks around and Latios is glowing. They touch each other�s hands and Latios drifts off towards the top of the sky. A streak of light forms then disappears.

Jessie, James, and Meowth then get washed away and everything turns back to normal. The two fossil pokemon become extinct again.

Annie and Oakley start to talk in a box. The box closes and they are trapped in there.

The group sails on a boat to look for Latias and Latios. A few pokemon come and bring Latias to them. Latias opens its eyes and it says that the streak of light is Latios. Latios gave up his life to save the city. They then do the �sitesharing� thing again and they see the Earth in which they live on. The Soul Dew then appears on Bianca�s hand.

They put the Soul Dew back into the pool of water. They also say a prayer for Latios.

Ash then calls to Lorenzo stating that they are leaving. Lorenzo tells them that Bianca might still be here. Up in Bianca�s room, Bianca takes something with her. Since Bianca wasn�t there, Ash and co. head off. They then see Bianca and they pull over. Bianca hands something to Ash. Bianca then gives Ash a kiss. Misty wonders if that girl was Bianca or Latias. Brock then states that he is very jealous. Ash takes a look of what Bianca gave to him and it�s a picture of Ash and Pikachu. The boat then takes off and they leave Altomare.