Ash, Pikachu and Brock take a break by the lake while Misty heads deeper into the forest with Togepi. As Misty picks a flower, Togepi wanders over to a very strange looking bush, it appears to have spider legs. Summoned by Misty's shrieks, Ash and Brock discover an Ariados in the bush. Just then, the Ariados's Trainer Aya, the sister of Fuchsia Gym Leader Koga, arrives. She explains that she's training with her Ariados to learn Pokémon Jujitsu. Under the guidance of a Tōkichi, the Sensei of a Dojo, who is the true owner of Ariados, she is trying to perfect her skills in Pokémon Jujitsu alongside her Venonat. Accepting an invitation from the Sensei, the group joins Aya for a day at the Pokémon Jujitsu Academy.
Donning special uniforms, red-colored for battle technique studies, which Ash chooses, yellow-colored for the technical class, which Brock chooses, and blue-colored for beauty-classes, which Misty is assigned. Initially reluctant to attend a beauty class, she swiftly changes her mind when told that the beauty treatments taught can make her look like a movie star. To her horror, the treatment involves Spinarak webbing applied to the face as a moisturizer. Meanwhile, Brock and his Pineco impress the class and its teacher with their highly synchronized battle demonstration. In Ash's class, he and Aya have a rematch of their battle at the Fuchsia Gym. Ash uses his Bulbasaur against Aya's Venonat, and initially, the battle follows the same pattern as their previous match, with Bulbasaur using his powerful Leech Seed attack to simultaneously trap and drain Venonat's energy.
However, Venonat shrugs off the Leech Seed and nearly wins the battle with a Supersonic-Tackle combination. Demonstrating Ash and his Pokémon's ingenuity and understanding of each other, Bulbasaur uses his Vine Whip to push himself high into the air, and then at Ash's prompting, uses Vine Whip to attack Venonat from the air, winning the match. Meanwhile, Team Rocket observes the battle and decide to steal the many rare Pokémon present at the school. Later, when everyone is going to sleep, Pikachu hears a noise from outside, so Ash goes to investigate and he finds Aya training. They contemplate their futures as Trainers until Venonat notices a strange occurrence. They find Poké Balls of most of the Trainers at the center to be stolen. Moments later, Team Rocket reveals themselves as the thieves. They grab Pikachu and trap him in a metal cage to prevent the effectiveness of his Electric attacks.
As they take flight in their balloon, the Sensei utilizes his glider to intercept Team Rocket and sabotage their balloon. He drops the Poké Balls to Ash and friends below and then falls from the balloon. Exhausted by the pursuit, and Ash's Pikachu still trapped in a metal cage, the Sensei and Ariados cannot battle Team Rocket, leaving it up to Aya. She worries that she is not prepared to battle Team Rocket, though is assured by the Sensei that no one is ever fully ready for battle. Ordering her Pokémon to use Rest, she makes a gamble that her Venonat will be able to endure. The ploy works. Upon waking, Venonat uses Tackle and Stun Spore, stunning Arbok. Ash finally succeeds in removing Pikachu from the cage, and returns to beat Jessie and James's final attack.
Aya reflects upon her choice to take a chance, and is praised by the Sensei for her turning "weakness into strength". When Ash and friends prepare to leave, the Sensei thanks them for their help, and promises them a place in his Dojo should they ever return.