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Ash and Misty both start by entering a race which involves water Pokemon pulling them along on a small boat-like board.
 Latias seems to take a liking to Ash and helps Totodile pull him faster than the rest of the competitors. It soon takes what seems to be a deliberate wrong turn, throwing Ash Pikachu and Totodile onto the land. 
Misty however, takes the lead and wins, beating a boy called Ross takes them around the town, telling them of a story about the guardians of Alto Mare, being Latios and Latias. Meanwhile, Annie and Oakley, two Team Rocket agents are tracking down Latios and Latias, by using technology which can detect a Pokemon, even when hiding in human form, and spot Latias.
 Latias runs into Pikachu, who appears to be thirsty, and so she turns on a tap for it to drink and cool down from. Ash runs after Pikachu and Latias seems intrigued by Ash, staring at him closely then runs away playfully. Unfortunately, she runs close by to Annie and Oakley, who chase her with an Ariados and Espeon. Pikachu senses danger and leads Ash after Latias, who fights them away with Pikachu's thunderbolt, then leads her away to safety.
 She then takes Ash and Pikachu to where Brock and Misty are waiting for him, then disappears. Ash, Brock and Misty are spotted to be looking in the museum, where Ash spots a girl who looks like Latias, mistaking her to actually be Latias. She walks away without realizing, and brushes Ash away when he tries to call her. Latias then appears and runs away to her home, where Ash and Pikachu follow. 
Latias brought him there to play, but Latios thought he was trespassing, about to attack when Latias steps in the way. The girl Latias had taken form of tells Latios to attack, but her grandfather stops them before Ash is hurt. Latias then takes Ash on a swing, where he rudely asks why she is named after a Pokemon. She shows her true form, causing him to fall off in shock, and she shows him some of her and her brother's powers.
Ash comes to learn that an orb called a soul dew is the power that keeps the city safe, and Latios and Latias protect it. It was created by the previous Latios sacrificing itself, and so hence the name Guardian of Alto Mare. 
The Soul Dew can also be used as a defense mechanism, which is found in the museum ash had been in earlier. When Ash leaves, Annie and Oakley use this time to strike upon Latias and Latios. They manage to capture Latios, but Latias runs away to find Ash for help. Annie and Oakley take the Soul Dew as their instructions order, and take Latios to the Museum. 
They place Latios into the defense mechanism and it levitates him up ready to be used. They place the Soul Dew in the machine, and it begins to work. Ash finds his way to the museum after some harsh battles, with help of Latias. 
Latias attempts to break the cage Latios is captured in, and just manages to get her head in to comfort him. Ash helps break Latios free, and the defense mechanism stops. Annie then picks up the Soul Dew and the defence mechanism goes out of control. 
The waters of Alto Mare begins to suck outwards, then rages towards the city in a huge tidal wave. Latios and Latias agree that they have to stop it, and Latios sacrifices itself to create a new Soul Dew, saving the town from destruction. The city returns to normal, and Ash places the Soul Dew where the previous one was. 
As Ash and his friends are about to leave, 'Bianca' hands Ash a painting of him and Pikachu, then he receives his first kiss. Brock appears to be very jealous, but Ash seems stunned. Whether the girl was Latias or Bianca is an argument that seems will never be resolved, but either way it can be used as evidence for Altoshipping or Mareshipping. 

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