Ash and his friends are returning to New Bark Town, but before Ash is able to get there to register for the Johto League Championship, Professor Elm sends him on an errand to retrieve a Pokémon Egg at the Marine Pokémon Laboratory. At the laboratory, the group meets a young researcher who is in a hurry. As she rushes past them, Brock's heart is sent aflutter and he chases after the woman, with his friends following behind. The researcher rushes to a pier and orders her Lanturn to use Supersonic. The sonar waves echo throughout the water, and the researcher watches intently for any responses. Brock suddenly arrives, but the researcher hushes him so that she can concentrate on her fieldwork. Suddenly the computer picks up the singing voices of traveling Lapras. The Lapras emerge from the water much to the delight of the group and the researcher.
As Ash watches the herd of Lapras from the shore, two adults separate from it, one of which approaches Ash. Ash realizes it's his old buddy, his Lapras that he caught in the Orange Islands, and its mother. The researcher is astounded and introduces herself as Naomi, a marine biologist and director of the Marine Laboratory. She reveals that Professor Elm told her that Ash would be coming to retrieve the Pokémon Egg. She takes everyone back to the lab, where she discusses Lapras migration. Naomi says that Lapras's travel routes appear to be linked to water temperature and season. She declares that the key to solving the mystery is in Lapras's voice. Then Naomi plays the traveling song that Lapras sing when they migrate and explains that her Lanturn's Supersonic can actually pinpoint their location. Meanwhile, Team Rocket spies on the Lapras herd from their Gyarados submarine. James suggests they capture the Lapras and rent them out as water taxi services. Jessie is thrilled with the money-making idea and declares full scheme ahead.
Later, Naomi shows the group the green-colored Egg and explains that it was rescued from a group of Pokémon poachers, where it was stolen from the Pokémon Preserve on Mt. Silver. She reveals that Professor Elm, who is the advisor of the Johto League Pokémon Preservation Council, will know exactly what to do with the Egg. Meanwhile, Lapras calls out for Ash to play with it. Misty and the others urge Ash to catch up with it, and so he leaps from Naomi's balcony down to the shore before him and Pikachu hop aboard Lapras. The trio enjoys a fun-filled afternoon surfing over the ocean waves. By night, Ash commends Lapras on its growth and increased power. Ash shows Lapras his eight Johto League Badges, however, the reunion is cut short when Team Rocket net Lapras's herd.
The Lapras cries also alert Naomi and the others, so they rush outside to examine the scene. Team Rocket's sub emerges from the water, and the trio performs their motto. As Ash and Lapras surf into view, James sends out Weezing for a Smokescreen. The acrid smoke leaves Ash coughing and allows Team Rocket to make a getaway with their hauled catch. Soon enough Lapras and Ash chase after the Rocket sub as Naomi urges Brock and Misty inside her own submarine. Team Rocket uses their secret booster weapons to bolster their speed, leaving Ash and the others in their wake. Noami pulls up beside Ash and calls for him to enter the sub while they follow after his Lapras.
Team Rocket is relieved that they have escaped Ash and the others. Suddenly something rocks their Gyarados submarine. Meowth points to the viewing screen and the Rocket trio watch in horror as the Lapras have gnawed through the capture net and making an escape. Jessie orders an emergency resurfacing to avoid any more losses. However, Jessie notices that there seems to be a significant lag and Meowth is unable to explain why. James suddenly spots a wall of riptides, but before they can act, Team Rocket and some of the Lapras are swept into the strong currents. Soon enough, Naomi's sub follows Ash's Lapras to the remaining herd. Naomi notices that a couple of Lapras are missing, Brock worries that the two missing Lapras might be caught in the rip. Ash's Lapras tells the herd to follow, saying it has heard something, but Naomi doesn't detect anything within the radar's range. The herd communicates with each other to guide their movements and fight the strong current while signaling for the missing two. Naomi suddenly gets something on her radar: the two missing Lapras replying to the herd's travel song. Naomi is amazed, realizing that they can distinguish the wordings of their song even when there is so much background noise and they can hear the songs of their friends from miles away, farther than radar can detect. Naomi notices that they are headed for a nearby island.
On the island, Team Rocket is exhausted but still have the two Lapras in the net. The herd suddenly appears out of the water and Naomi's submarine also resurfaces. But before they can retrieve the two missing Lapras, Jessie and James send out Arbok and Weezing. Brock chooses to send out Crobat to battle against Team Rocket. He orders Crobat to use Sonic Boom which hits Weezing and Arbok. As Naomi and Misty strive to release the two, before doing so, Meowth rushes in to stop them with his claws. Though Ash has Pikachu knock Meowth out of the way with a Quick Attack. Ash, Misty, and Naomi release the two and Lapras and its mom are happy to be reunited again. Arbok and Weezing were ready to attack, but they're stopped by the herd of Lapras, as they, along with their leader use Ice Beam to freeze Team Rocket's Pokémon. Ash commands Pikachu to use Thunder to blast Team Rocket off. The herd of Lapras is now safe.
By daybreak, Ash and his friends farewell the Lapras herd. They watch as the leader of the herd asks Ash's Lapras to take over the lead, and it accepts the honor. Naomi explains to the group that the leader was so impressed by how Ash's Lapras had taken charge of the situation the day before that it decided to "hand over" its leadership duty. Lapras turns its head to say goodbye to Ash before it and its herd continues on their migration route. Later, Naomi reports back to Professor Elm that she can finally complete her thesis on Lapras migration patterns. Elm turns his attention to Ash, who is holding an Egg case with the Egg inside, and asks him to escort the Egg back to his New Bark Town lab. Ash takes up the task. He and his friends say goodbye to Naomi and her Lanturn before continuing to follow the eastern Johto shore to New Bark Town.