The Breeding Center Secret is the 57th episode of the Indigo League season.
When Ash and his friends take a break in a nearby city, Todd Snap decides to use the opportunity to take pictures. However, they are interrupted by a giant plasma screen, which informs them of the opening of a Pokémon Breeding Center. Snap informs Ash that Breeding Centers are places where Pokémon are given relaxing treatments, which can even prompt evolution. Ash is ecstatic about the opening, proclaiming that he wants to visit. At the entrance to the Breeding Center, a large crowd has formed.
Ash and his friends arrive, and Brock immediately goes into raptures over the owner, Cassidy. Inside the Center, Misty begins interrogating Cassidy about how they treat their customers' Pokémon. She gives her Psyduck to Butch and Cassidy, who ask whether she would like any special treatment for it. Misty comments that they should knock some common sense into it, as they place Psyduck onto a conveyor belt. After they walk around, Ash asks whether Misty is just going to abandon Psyduck at the Breeding Center, which she denies.
Snap's attention is caught off guard by a restaurant, and the group notices that everything at the restaurant is free of charge. The chef walks through the door, informing Ash that all they need to do in order to eat for free is to show him his favourite Pokémon. After Ash releases his Pokémon, the chef informs him that his favourite Pokémon is not one of them. When Brock and Misty follow suit, the chef reveals that his favourite Pokémon is not with them either. The chef takes out a photograph of the Pokémon, which is revealed to be a Psyduck.
Misty and the others rush back to the Breeding Center to retrieve Psyduck, only to find it closed. When Misty enters through the back door, they find themselves walking through an abandoned building. As they enter one of the rooms, they discover all of the Pokémon trapped in cages. Brock comes across Psyduck, but is alerted to one of the cages being transported to a separate room. Butch and Cassidy confer that the Sandshrew is only useful to them if it can learn Fury Swipes. They proclaim that their boss will give them a bonus once he hears of their exploits.
Ash and the others overhear their conversation, as Snap formulates a plan to incriminate them by taking pictures of the operation. Giovanni then appears on a screen before Butch and Cassidy, demanding the progress of their operation. They confirm that it is going as planned, to which Giovanni proclaims that if Jessie and James had been notified of this operation they would have messed it up. As Snap takes pictures of the imprisoned Pokémon, Butch notices the flash from the camera. Butch leaves the room to look around in the bay, but finds no one there.
However, he brushes it off when he sees a Pikachu discharging electricity. Ash and the others emerge when Butch leaves, but Misty refuses to leave Psyduck trapped in its cage. However, Ash and the others are forced back into hiding as Jessie and James forcefully enter the bay. Jessie states that they are going to steal all of the Pokémon. James attempts to pick the lock, but is startled by Ash and the others, who ask what they are doing here. Team Rocket poses the same question, assuming they too are here to steal the Pokémon.
Suddenly, the lights flicker on and Butch and Cassidy appear before them. The duo then copy Team Rocket's motto, reciting it. After Team Rocket accuse them of copying their motto, Butch states that Giovanni will be mad after hearing that they have stolen his Pokémon. Whilst Jessie and James beg for their jobs, Ash and the others sneak out into the other room. However, Cassidy stops them, stating that they cannot leave. Team Rocket also run away, but not before James notices his Weepinbell has evolved into a Victreebel.
However, both Team Rocket and Ash and his friends are captured in cages. Misty and Pikachu escape, as Butch confiscates Snap’s camera. When Officer Jenny arrives on the scene, Cassidy pretends to pout over the situation, whilst Ash and the others are brought to the station house. The next day, Misty attempts to get her Psyduck back from the Breeding Center. Whilst Pikachu searches for Snap's camera, Cassidy hands her Pokémon back. Misty then runs from the Breeding Center.
Meanwhile in prison, Ash and the others try to plead their case to Jenny. Misty interrupts them, showing Snap's photos to her. When Jenny returns to the Breeding Center, Butch and Cassidy are caught off guard and resort to fleeing after their Raticate is defeated. However, Ash uses his Bulbasaur to bind the two criminals. As Butch and Cassidy are sent to prison, Jenny thanks them for their assistance. Back at the restaurant, Misty helps herself to multiple servings of ice cream. Back in prison, Jessie, James and Meowth complain about their cell whilst digging out. Ash and Snap part ways, with Ash and his friends heading to Cinnabar Island and Snap heading to the mountainside. As Ash and the others continue on their way, Team Rocket is digging directly underneath them.
- When Ash and his friends demand to know why Team Rocket are also in the Breeding Center, Jessie's lipstick is noticeably missing.
- This is the first episode to introduce Pokémon Breeding Centers, where Pokémon trainers can leave their Pokémon and help them gain experience.
- This the last episode to end with the PokéRap song.
- First appearance of Butch and Cassidy.
- James's Weepinbell evolves into a Victreebel in this episode, despite the fact we never saw him initially catch a Weepinbell.
- When the gang goes back to get Psyduck, they forget their backpacks on the sidewalk.
- The "Who's that Pokémon?" in this episode is Psyduck.
"It's an outrage! It took us months to find a motto we could swipe!" ~ Meowth upon finding out that Butch and Cassidy stole their motto.
"A little love power works miracles" ~ Cassidy reciting the motto of the Pokémon Breeding Center."
"We believe in love power, because we love power." ~ Cassidy and Butch.