Ash's friend Richie has come to Professor Oak's lab to ask for advice, but Tracey is the only one home; the Professor is on Seafoam Island for a live TV appearance. At least, that was the idea—when Tracey calls for an update, DJ Mary tells him that Professor Oak has vanished! Tracey and Richie head to the TV station to find out what happened. According to DJ Mary, Professor Oak made it to the morning rehearsal, but after two strangers pulled him away to ask a question, he was never seen again! Security didn't see the Professor or the strangers leave the station, but Richie realizes that the kidnappers posed as deliverymen to get in and out of the building.
Indeed, it's just as Richie thought, and Butch and Cassidy are the ones behind the plan. Dr. Namba wants to force the Professor to tell him where to find Pokérus. Namba needs samples of the Pokérus virus to help him with the Pokémon Power Acceleration Project, but Oak refuses to give up the information. To get him to talk, Butch and Cassidy torment him with the sound of a nail on glass. But Richie sent his Taillow, Rose, to look for a suspicious delivery truck, and that leads the good guys straight to Team Rocket's hideout.
When the rescuers burst into the hideout, Cassidy and Butch use Sableye and Mightyena to battle Tracey's Scyther and Richie's Pikachu, Sparky, while they grab the Professor and run for it. Tracey's Scyther is defeated, but Richie sends in his Charmeleon for additional firepower. Between that and Sparky, it isn't long before Butch, Cassidy, and both of their Pokémon are blasted into the sky. With Officer Jenny's help, Professor Oak and DJ Mary are back in time for their live TV show, and Richie even has an invitation to visit the Professor's lab and help him out: a happy ending for everyone!
It is a quiet day at Professor Oak's lab when Tracey hears the doorbell. He opens the door to see Sparky. The camera scrolls up to show Ritchie who introduces himself. Tracey remembers hearing about Ritchie from Ash, and invites them in. Ritchie explains that he has come to get advice from Professor Oak on the best way to evolve his Eevee. Tracey confirms that the Professor would be the best person to ask, but that he is currently at the Seafoam Islands, and won't be back until that night. Tracey decides to call Professor Oak on the phone, but learns from Mary that Professor Oak has vanished without a trace.
One hitchhiking lorry ride later, Tracey and Ritchie arrive at the Seafoam Island TV Station. The security guards tell them that is temporarily closed, but Mary explains that Tracey is Professor Oak's Assistant. Tracey then introduces Ritchie as Oak's nephew. Inside, Mary explains that Professor Oak disappeared half way through a rehearsal. He is nowhere in the building, and yet the security guards haven't seen him leave. Ritchie asks Mary to tell them what happened, and Tracey introduces him.
Mary explains that they had arrived early so that they could rehearse before the show aired live that evening. Everything had gone well until they had taken a break for lunch. Professor Oak invited Mary to lunch but while they were waiting for the elevator, two funny-looking scientists approached them. They tell the Professor that they have something rare that might interest him. The elevator doors opened, so Professor Oak offered to see Mary downstairs. That was the last she saw of him. Ritchie guesses that the scientists had something to do with it, but Officer Jenny tells him that no one else has seen the scientists in the building, including the security guards.
Outside, Ritchie establishes that the only way out is through the front doors. There are doors at the back and on the roof, but they haven't been opened all day. Ritchie thinks for a moment, and then asks the guards if any large package has been brought in. Ritchie explains his theory: One person came in with a large package. Inside, a second person came out and they put Professor Oak inside. Then, they walked out the front door. The security guards says there was one delivery earlier that morning. Butch had brought in a Nidoqueen costume, supposedly as a prop for Funniest Pokémon Home Videos. Ritchie thinks it sounds like this is who took Professor Oak.
The scene cuts to a lorry going along a road. Inside, Professor Oak is tied up. Butch and Cassidy complement each other on a job done smoothly. The scene cuts to after Butch got inside the building, and Cassidy is revealed to have been inside the Nidoqueen. Dressed up as scientists, Cassidy advises Butch to use lots of big words. After Mary gets on the elevator, Cassidy tells Professor Oak that they had found a strange Pokémon Egg in the Hoenn region that could be a new species. After walking into a room to talk in private, Butch opens the box and Professor Oak leans in for a closer look. Suddenly, it opens up and a model of a Bulbasaur sprays a pink gas into Professor Oak's face.
As one went in and two went out, leaving with the same stuffed Nidoqueen, it is obvious to Ritchie that they are the ones who took Professor Oak. The security guard tells them that the lorry they left in had a marking of a Pidgeot. As the only way off the island by road is the bridge back to Fuchsia City, Ritchie gets Officer Jenny to set up a road block there. They then head over there in a police car.
Meanwhile, Butch and Cassidy remember being nervous when Professor Namba called them to see him. He asks what they are willing to do for Team Rocket, and Butch replies, "Anything, sir". He then tells them that the Pokémon Power Acceleration Project is a secret project he has been working on for years. However, he is stuck and does not know how to proceed. He needs information from Professor Oak, so he tells Butch and Cassidy to kidnap him. Now, they are heading towards the rendezvous point so that the Professors can have their meeting.
Meanwhile, the police car is at the bridge where Officer Jenny learns that the truck hasn't passed through the checkpoint yet. Ritchie sends out Rose, his Taillow, and Tracey comments that Ash has a Taillow too. Ritchie says that he and Ash tend to catch a lot of the same Pokémon. Ritchie tells Rose to search for the truck, but Rose does not know what a Pidgeot looks like. So Tracey quickly makes a sketch for Rose. Rose flies off.
In an abandoned warehouse, Professor Oak is awake, though ties to a chair. Butch contacts Namba through a big screen. Professor Namba explains to Professor Oak that the mysterious viral lifeform Pokérus is an important component of the PPAP, which make ill Pokémon evolve at a faster rate. However, all of his specimens have died out. So he tells Professor Oak to tell him everything he knows about Pokérus and where it grows. Professor Oak refuses to talk, so Butch and Cassidy start the torture by scraping a nail across a piece of glass. Once Professor Oak has finished screaming, Cassidy asks if he is ready to talk. Professor Oak states that he will never talk, so they do it again.
Rose hears Professor Oak's screams and heads back to Ritchie. On seeing Rose, Officer Jenny starts driving towards the warehouse.
The chair Professor Oak is on has now fallen on its back. Faced with another screeching, Professor Oak begins to talk. He stalls by giving the name derivation, but then Rose flies in and crashes into the glass, shattering it. Turning, Butch and Cassidy see the rescue team at the door. Cassidy tuns off the connection, and then tells Butch to get ready to run. Meanwhile, Tracey and Ritchie recognize them and, after Butch gets annoyed for being called Botch, Ritchie tells them to hand the Professor over. Cassidy refuses and the two pick up Professor Oak and run out the back door. Ritchie sends Sparky forward, but Cassidy sends out her Sableye to attack with Scratch.
Ritchie and Tracey run after them, but Professor Oak is already being loaded into the lorry and Butch sends out his Mightyena. Rose uses Gust, but Sableye hits it with a Focus Punch. Tracey sends out his Scyther, which Mightyena attacks with Bite. Scyther then counters with Slash, and Mightyena then uses Tackle on Scyther. As Mary calls to Tracey to be careful, Mightyena uses Iron Tail on Scyther, and so Tracey returns it.
Ritchie sends Sparky into the battle, and Sableye uses Fury Swipes on both it and Rose. Ritchie returns Rose and tells Sparky to step back. He then sends out Zippo the Charmeleon to use Flamethrower. Mightyena jumps aside, but some stray embers land on Professor Oak's head. In pain, he runs past everyone and right into the wall! Butch and Cassidy run over to get him back, busying Ritchie's Pokémon by sending their own Pokémon in to attack. Sparky uses Thunderbolt on Sableye, who falls on Mightyena. Zippo then uses Fire Spin on the two of them, sending them into Butch and Cassidy. Sparky finishes with Thunder, sending Butch and Cassidy blasting off.
Professor Oak is alright, but Mary worries that they won't get to the live broadcast in time. Officer Jenny promises to get them there, and the scene cuts to them recording Pokémon Masterchef in front of an audience. Later, Professor Oak asks what brought him around, and Ritchie asks if he can stay for a few days to get help with his Eevee. Professor Oak says he can stay around for a few weeks if he likes, and asks if Ritchie could help him to set up a security system at the ranch (contradicting a statement he made a couple of episodes ago, when he said the Pokémon were the only security system they would ever need). Mary calls them over to be contestants on I Wouldn't Eat That if I Were You. That night, both boys went to bed with a stomachache, but Professor Oak stayed up to research Pokérus in order to try to discover Team Rocket's plans for it.