As our heroes and Alexa wrap up their shipboard tour of the Decolore Islands, they spot several Pokémon native to the Kanto region. Porter says that’s a sure sign that their final stop, Vermilion City, is close by! They all have plans for Kanto: Ash can’t wait to get home, Iris and Cilan really want to see some Pokémon that are new to them, and Alexa has plans to interview Professor Oak.
Of course, Team Rocket is close behind, and the villains have plans of their own—to finally capture Pikachu! From their Basculin submarine, they try to stop the cruise ship by entangling its propellers, and when that doesn’t work, they succeed in floating the ship up into the sky with giant balloons! The passengers panic, and in the confusion, Team Rocket manages to net Pikachu, Axew, and an impressive haul of Poké Balls from our heroes and the other passengers!
Trapped in the cargo hold, Ash, Iris, and Cilan make several attempts to escape before they’re successful, and then come at Team Rocket with a vengeance! It isn’t long before the hapless trio is overpowered, and all the Pokémon are safely returned, as the ship glides down to a safe and gentle splashdown. Alexa has been working in her cabin with headphones on the whole time, so she has no idea of what’s been happening—but when she finds out, she wants to write an article about it!
The Decolore Queen finally docks in Vermilion City, and Iris and Cilan can’t contain their excitement—they want to set out on the next leg of their journey right away! Iris wants to go to Blackthorn City to train with Gym Leader Clair, and Cilan plans to attend a fishing competition in the Hoenn region. Ash and Alexa go to the train station to see them off, and as they say goodbye, it’s a bittersweet moment as Ash thinks back on all the adventures they’ve had together.
But after a long journey, he’s nearly home, and it’s time for Ash and Alexa to set off for Pallet Town!
Now very close to the Kanto region, Ash, Iris, and Cilan watch a Gyarados from the side of their boat and talk about how excited they are. Meanwhile, Alexa walks up and is surprised to discover that Ash knows Professor Oak, with whom she hopes to have an interview. Later, while Alexa is in her cabin working, Team Rocket is following behind the boat in their Basculin submarine. They launch an attack on the boat, using two hooks to stop the propellers. However, when they attempt to pull the ship, the propellers begin spinning again and leave Team Rocket's submarine floating on the surface of the water, where Ash and his friends see it and mistake it for a real Basculin. With their first plan a failure, Team Rocket then attempts another assault from their hot-air balloon. They launch several missiles at the boat that burst open to reveal strong hooks. As the hooks attach themselves to the boat, a balloon begins to inflate from each one, lifting the boat out of the water and into the sky. While everyone else is in a panic, Alexa is too absorbed in her work to notice anything.
On the deck of the boat, Porter attempts to restore order while Ash, Iris, and Cilan confront Team Rocket. Jessie and Meowth descend from the balloon, with Jessie disguised partially as James and reciting the entire motto by herself. Meanwhile, the real James disguises himself as Porter and tricks the group into taking out their Poké Balls, resulting in Meowth using a special vacuum-like device to steal them all. James then uses a net to snatch Pikachu and Axew, revealing himself to be a fake after the real Porter arrives. As the group tries to rescue their Pokémon, Frillish and Amoonguss use Bubble Beam and Hidden Power, respectively, to create a small explosion that sends Ash, Iris, and Cilan flying into the ship's cargo hold. Taking their advantage of having the twerps out of the way, Team Rocket tries to steal all of the other passengers' Pokémon; however, Porter intervenes and is nearly thrown overboard by another attack by Frillish and Amoonguss. Team Rocket then proceeds to continue stealing all of the Poké Balls on the ship.
Back in the cargo hold, Ash, Iris, and Cilan use the many boxes lining the walls to create a stairway in order to reach a hook that they can use to escape. As they try to climb out, it collapses and Ash grabs onto Cilan while still holding the hook at the top of the hold. Cilan, similarly, is keeping Iris from falling, and the latter begins swinging back and forth to give them the boost they need to escape. Just as Team Rocket is about to escape on their balloon, the three of them soar into the air and bring all three Rockets back down to the boat, retrieving their Poké Balls and attempting to free Pikachu and Axew. After Charizard makes quick work of Frillish and Amoonguss, Ash manages to get Pikachu and Axew out of the net and Team Rocket is sent blasting off. Snivy uses Leaf Storm to cut the balloons and lower the boat back to the water while the passengers rescue Porter. It is only when the boat impacts the water that Alexa notices anything and looks up from her work, wondering what had happened.
After the boat docks in Vermilion City, the group shares a meal at a local restaurant. Iris and Cilan both express their wishes to start on their new journeys right away, with Iris wishing to go see Clair in Blackthorn City and Cilan wanting to participate in an Old Rod Fishing Rally hosted by Mr. Briney. Ash tells them he understands, albeit a little sadly. Ash and Alexa go with Iris and Cilan to the train station, where their long journey comes to an end and the three friends, as well as Axew and Pikachu, share a bittersweet goodbye. As the train pulls out of the station, Ash calls after his two friends to have a great trip and recalls all of the experiences the three of them shared together.