Just as if the trouble caused by Oakley wasn’t enough, Aerodactyl managed to spot Latias and grabs it with its claws! Pikachu uses Thunderbolt to shock Aerodactyl, who then uses Hyper Beam on the boat! Latias manages to get Ash out of the water, then goes back on their boat, and the chase continues! Meanwhile, Misty and Brock release their Crobat, Politoed and Corsola and asks them to go help Ash while Brock climbs on the iron wires.
Aerodactyl crashes on a building tue to its huge size, but then comes Kabutops, slashing multiple times, trying to hit Ash and Latias. Ash is knocked on the wall and when he’s about to get finished, Crobat tacles the fossil Pokemon while Corsola and Politoed uses water attacks to knock Kabutops into the water. Back in the museum, Oakley cackles as the city is under her control, while Latios is badly injured and gets hurt more as Oakley uses the machine’s powers. Then, she spots Ash on the water with Latias. She decides to create a typhoon which spills tons of water, while Ash and Latias runs to the museum.
But Oakley then create a barrier made of water, which then become a huge whirlpool, engulfing Ash and Latias! As Ash and Pikach are about to drown, Latias’ eyes glow blue and dispels the false water generated bu the machine. Then, in the Museum, it get haywire, locking Oakley inside and harming Latios even more than before! Fortunately, Ash manage to free Bianca and Lorenzo, who are determined to stop the machine before it’s too late. Latias find its companion with serious injuries, and as mush as Ash and Latias tackles the rings, it doesn’t do a thing.
However, Latias managed to get hits head inside the rings, allowing the gang to pull off Latios out of there. The two Eon Pokemon falls on the ground along with the rings…then the machine stops. The whole gang then gets reunited, while Annie checks out the Soul Dew ; it has a dark-purple like color. She touches it besides Lorenzo’s warning, get knocked into the machine as the Soul Dew explodes!!! The machine goes haywire again, and Lorenzo re-tells the prophecy ; if some with an evil heart uses the machine, the Soul Dew will die… along with the city itself! Water is getting away, leaving gondolas and boats on dry land.
As the gang gets out, there’s no more water…but it will come back. A rumble is then heard, and the waters returns as a huge tidal wave!!! Latias and Latios then flies away near the tidal wave, knowing what to do. Latios then uses its Memento attack, separating the waters in two, then, the waters gently falls back. As Latias wakes up in the ball of light, it sees Latios in the same color as the Soul Dew, then understands what happened ; the Memento attack killed Latios, who becomes a beam of light, then dissapears. The waters returns, the city comes back to normal, the prehistoric Pokemon becomes fossils once again while Anie and Oakley are bickering in the machine about the fact that Annie evolved Oakley’s Gloom into a Vileplume rather than Bellossom in kindergarten. During this time, Ash and the gang calls out Latias and Latios’ names, and sees Latias on a Mantine. Latias wakes up, then Bianca asks about Latios. Then Lorenzo undersands what happened during that night.
Everyone is sad, but a Sight Sharing shows the gang the blue planet we live on, then, the light becomes a new Soul Dew. Latias cries, sure, it lost its sibling, and Lorenzo puts the Soul Dew back to the pool, and everything turns back to normal. As Ash and his friends are leaving Altomare, Bianca comes to Ash with a small gift, a painting of him and Pikachu. She then kisses Ash without a word, while Misty wonders is this was Bianca…or rather, Latias? In the ending scene, two Latios can be seen with Latias, either meaning two newborn Latioses came to Altomare, or they are the ressurected Latioses who died earlier. Everything ends well, and the thieves winds up in jail.