At Professor Oak's lab, Tracey and the Professor are busy with their daily work. So busy that they don't even notice when a Team Rocket helicopter lands on the property—Butch and Cassidy are here, and they plan to steal all the stored Pokémon from the lab! While Ash's mom Delia stops by to say hello to Professor Oak, Butch and Cassidy put on Pokémon disguises and make their way toward the lab. The local Pokémon take an interest in these new visitors, thinking they're real Pokémon, but an Oddish realizes the newcomers are just people in costumes.
Oddish alerts Bulbasaur, who decides to take action. It grabs Tracey and sends Noctowl to scout the area for signs of the intruders. By the time Tracey realizes what's going on, Butch and Cassidy have already looted the Poké Balls from the lab and left the building. Now they're back in their Pokémon disguises and headed for the helicopter, but they're slowed down by a lovestruck Nidoking and an affectionate Muk.
In the meantime, Noctowl has led Tracey to Team Rocket's hidden helicopter, and Totodile has told Professor Oak and Delia about the emergency. All the Pokémon are on the lookout for the thieves, too! Our heroes all surprise Butch and Cassidy before they can get away, but the villains won't give up. They send out Hitmontop and Houndour, so Professor Oak calls on Bulbasaur for help. And when Tracey's Scyther and Delia's Mr. Mime join in, it spells defeat for Butch and Cassidy, who end up being blasted into the sky. Now the Poké Balls are safe and peace has been restored!
Professor Oak and Tracey are so busy looking after Pokémon that they don't notice when a helicopter lands near the laboratory. In fact, Noctowl is the only one that does notice it. Butch and Cassidy step out their aircraft, covering it with a camouflage blanket and branches so to go unnoticed. After locating the lab, they discuss their plan: almost every Trainer who starts their journey in Pallet Town stores their extra Poké Balls there, so they are going to sneak in and steal them all. As Tracey and Professor Oak are the only people around, it shouldn't be very hard.
As Tracey returns from feeding the Pokémon, he hears the doorbell and goes to see who it is. It is the Magikarp salesman, who immediately tries to sell Tracey the Magikarp he has. He tells Tracey that the Magikarp lays golden eggs, making Tracey very suspicious. Professor Oak comes over to see what is going on, and becomes angry when he hears that the salesman is selling Pokémon. Tracey tells him that this is a Pokémon laboratory, and the salesman then makes a hasty exit. Professor Oak says that Pokémon should not be bought and sold. Tracey says they should report him to Officer Jenny, and then the doorbell rings again. Tracey, mistakenly believing that the Magikarp salesman has returned, says he will teach him a lesson, and starts harshly, only to realize his mistake when he sees that it is Delia and Mimey. Delia is stunned, admitting that she had bought some cookies. Tracey says that now was a great time for a break and invites Delia inside.
Elsewhere, Bulbasaur is enjoying a walk through the ranch. It smiles upon seeing a Jumpluff and Skiploom getting along. Bulbasaur then notices an odd-looking Golem and Nidoqueen, which are actually Butch and Cassidy in disguise. Totodile also notices them, then dances and douses the pair with a Water Gun. Butch kicks it away in frustration, but Totodile retaliates with a more powerful Water Gun. Butch reflects it with a tool on hand, sending Totodile backwards. Butch and Cassidy take a moment to dry themselves. An Oddish notices the half-human, half-Pokémon things, and runs off to tell Bulbasaur. However, by the time the two get there, Butch and Cassidy have already set off again. Cassidy stands on Cyndaquil, who was taking a nap, and it sends up a huge fire in defense. Butch uses a fire extinguisher on it, and the two leave, just as Bulbasaur and Oddish catch up to Cyndaquil.
Back at the lab, Delia asks Professor Oak if he has heard from Ash. Oak tells her that he has just reached Petalburg City. Delia comments that she loves Petalburg City, and that she hopes Ash captures a Zigzagoon. At this moment, Bulbasaur gets her attention by tapping on the window. Oak tells Delia that he is busy, so she informs Bulbasaur that the Professor is unavailable. Bulbasaur then wakes up Noctowl, and Noctowl flies off to search. Bulbasaur rushes over to Tracey for help, and forcefully pulls him away from feeding the Jumpluff.
Bulbasaur is right to rush, as Butch and Cassidy have now reached the lab, though not before being noticed by Noctowl. As Butch cuts a hole in the window, he comments that Giovanni will be so pleased that they will get a major promotion. Cassidy reaches through the hole to unlatch the window, and they enter the lab. They comment on how much better they are than "Messy" and "Lames", which they find so funny that they laugh manically. Remembering where they are, they shut up and start looking around. Butch and Cassidy soon sneak into the Poké Ball room, which has no security alarms surprisingly. Meanwhile, Noctowl guides Tracey and the others over to the damaged window. He immediately rushes over to Professor Oak to tell him that someone has broken in. They search the lab until they reach the Poké Ball room, where they are shocked to see that all the Poké Balls are gone. Tracey says that whoever did this must be professionals. Professor Oak says that it must be Team Rocket's work, but Tracey doubts this as the Team Rocket he knows couldn't pull it off without messing something up.
The Pokémon begin to spread the word. Bayleef tells Heracross. Bulbasaur tells the Skiploom and Jumpluff, who tell the Oddish and Bellossom, who tell Kingler, who tells four of the Tauros, who stampede to wake up Snorlax. As all the Pokémon search, Butch and Cassidy make their escape in their costumes, with the Poké Balls inside a container covered by a a Muk cloak. However, a Nidoking spots them and tries to hug Cassidy. When they manage to lose that, Muk turns up and smothers the Poké Balls. Meanwhile, Noctowl locates the helicopter and rushes off to tell Tracey. Muk has now covered both Cassidy and Butch, who can't get up. Then Totodile turns up and uses another Water Gun. It jumps aside from the reflector, and uses another one to knock Butch into a tree. They take this chance to run off, which makes Muk sad, but Totodile happily runs off in the opposite direction.
Bulbasaur uses its vines to uncover the sheet covering the helicopter while Totodile tells Delia and Professor Oak where Butch and Cassidy are. As all the Pokémon rush over to the spot, so do Butch and Cassidy. For a moment, they think they have made it, but then Tracey steps forward, barring the way. Professor Oak and Delia come in behind them, and tell them that they are completely surrounded. Tracey tells them to give up now, or they are in big trouble. Butch and Cassidy proceed to recite their motto. Tracey vaguely recalls the other Team Rocket. After Butch gets annoyed at Tracey and Delia for calling him "Biff" and "Bill" respectively, Professor Oak tells them that they can't steal Pokémon, as Pokémon must be earned. Butch and Cassidy refuse and send out Hitmontop and Houndour. Bulbasaur steps forward to battle, and Oak recognizes Bulbasaur as one of his oldest companions. Tracey sends out Scyther, while Delia sends Mimey forward.
Houndour starts off with Ember, which Mimey reflects with Light Screen. Hitmontop then uses Rolling Kick, but it does nothing to the Light Screen. Next, Bulbasaur and Scyther attack Hitmontop with Vine Whip and Quick Attack respectively. While they are busy, Cassidy orders Houndour to use Bite on Mimey, but Mimey Double Slaps it back. Butch orders Hitmontop to use Rapid Spin on Bulbasaur, but Bulbasaur reflects it with another Vine Whip. Hitmontop slams into Butch and Cassidy, and is then hit by Scyther's Cut attack. After complimenting Scyther, Oak orders Cyndaquil to use Flamethrower, which engulfs Team Rocket. Bulbasaur immediately comes in with a Solar Beam which causes an explosion. While Cassidy contemplates that things are not good, Oak comments that Pokémon are sometimes inspirational. Totodile wants to join in, so it uses its strongest Water Gun of the day, making Butch and Cassidy blast off.
All the Poké Balls are accounted for. Oak comments that while the lab doesn't have an advanced security system, the Pokémon are all the protection that they will ever need. The humans thank the Pokémon and the Pokémon cheer. Later, Oak reads his completed love poem, which Delia felt for sure that it was about her, but then, so did Bulbasaur.