Ash, Misty, and Tracey are yet again riding on Lapras as it propels them towards the next island. Since Ash has won the championship (he's still gazing at the trophy in awe), they're heading back to Pallet Town. Suddenly, Lapras turns sharply and swims rapidly in a different direction. In the distance, Ash and his friends spot a large school of Lapras. As Tracey sketches, the idea comes to him that these Lapras could be the school that Ash's Lapras had gotten separated from months ago. Ash thinks back to that time when they first met and he had to earn its trust. He then remembers his promise to help it find its family again.
As Lapras draws closer, however, the school of Lapras looks at it and hurriedly starts to swim away. One lighter colored Lapras looks back, but another larger Lapras pushes it along. Ash yells at them for abandoning their friend and the larger Lapras sprays a Water Gun at them. Tracey notes how unusual this is, as Lapras don't usually attack humans in the wild. The larger Lapras then uses Mist and the school swims into the distance. Devastated, Ash's Lapras calls out one more time in tears
When Ash and his friends get to the next island, they call Professor Oak and ask him what he thought. He agreed that it was unusual and concludes that the Lapras were afraid of people for some reason. When Misty asks who would do such a thing, Officer Jenny comes up behind them saying that it could be pirates. She explains that the area around the island is a Pokémon No-Capture Zone but that a group of pirates have been poaching in the area. She says that they call the lead pirate Captain Crook. Ash tells her that this sounds like the work of Team Rocket and tells Jenny about the three.
Suddenly, voices ring out from behind the emergency room doors of the Pokémon Center. The doors open and reveal a very bandaged trio who do their motto but then curl up into a fetal position. Ash yells at them for poaching, but they tell him and the rest that it wasn't their doing. In fact, they're in the hospital because of Captain Crook and his gang. They tell about how one of his cannonballs exploded their sub out of the water and into a cliff. Ash tells them that they deserved it to which James and Meowth agree (only to be hit by Jessie's crutch). Officer Jenny tells them to come down to the station and fill out a report and check on their own file, but they run off, saying that they've been miraculously cured.
Meanwhile, the school of Lapras is swimming near the island. The lighter colored one from before is looking at it sadly, but the larger one, apparently the leader, swims in front of it and shakes its head. As they start to swim away, Captain Crook and his crew sight them. Crook tells his first mate to ready their "secret weapons."
Ash and his friends set off to catch up with the school, as they don't want to give up. Tracey asks Ash how he intends to let the Lapras know that they are friends. Ash tells them that all he'll have to do is put on a friendly face and everything will be fine. Misty suggests that they just tell them.
By this time, Captain Crook has caught up with the Lapras. He fires the cannons and out fly PokéBalls. When they land in the water, Tentacruel pop out. The Tentacruel use Poison Sting, but the attack is deflected by the lead Lapras's Water Gun. Crook fires more PokéBalls and more Tentacruel pop up in front of the Lapras. As Ash and his friends draw closer, they see the ship attacking the Lapras. Misty realizes that the pirates are forcing the Tentacruel to bully the Lapras. Tracey sends out Marill and they swim back to the island to get Officer Jenny.
As Ash and Misty surge closer on Lapras, Team Rocket propels their sub underneath them. They want to see Ash and Misty get paralyzed by the pirates and then steal Pikachu.
The Lapras are now completely surrounded by Tentacruel and look very worried. Crook orders a Poison Sting but just before they attack Pikachu shocks everything (including the Lapras and Ash and Misty). The Tentacruel get really angry and swim over, but Crook's ship sails between the two. Crook fires the cannons with real cannonballs this time, but Lapras is able to dodge them all. Ash and Misty send out all their water Pokémon who all use Water Gun and really smashes up the ship. Crook orders another round of cannon fire, but his mate tells them that they're all out. Crook stuffs him in a cannon and fires him into the water instead but, needless to say, it doesn't do much.
Meanwhile, Ash tries to aggravate the Tentacruel into attacking them instead of the Lapras. He manages to do so, and the Tentacruel start to chase them. Ash shouts to the Lapras to make their getaway now, but they seem reluctant to do so, especially the lighter colored one (I'm starting to think that that Lapras is Ash's Lapras's mother or something). While Team Rocket pedals right behind Ash, Jessie laughs about how their plan is working. James gives her an unfortunate reminder: if the Tentacruel are chasing Ash and Team Rocket is behind him, the Tentacruel will get to them first. As if on cue, a Tentacruel slams into the sub and it is flung into the air.
During this time, Misty has been able to round up everyone on the boat. She tells Captain Crook to call of his Tentacruel, but he refuses. The Tentacruel surround Ash and prepare to attack. Lapras hits a few with Water Gun, but then they all use Supersonic. Ash covers his ears in pain and Pikachu and Lapras are unable to fight as well. Suddenly, the Tentacruel are frozen on the spot by the school of Lapras. They swim up and Lapras and its mom nuzzle each other.
Later on, after Officer Jenny has arrived and arrested the men as well as Team Rocket. Misty tells the Tentacruel that they are free to go and they happily swim away.
Ash tells Lapras that its time to join its group. They both think back to the times they had and how important Lapras was on Ash's journey through the Orange Islands. Lapras dives under the water and lifts its trainer onto the boat. Ash gives it one more goodbye, and it swims over to its mother. As they swim away, Ash and his friends say goodbye. Ash's promise has been fulfilled