Ash and his friends arrive on Murcott Island, where Tracey brings out Marill and Venonat. He reveals that the island is famous for housing plenty of Bug types. Due to her fear of Bug Pokémon, Misty initially decides to stay on the beach, but when Ash tells Tracey of her fear and he taunts her by calling her a chicken, she changes her mind.
The group walks along, and Tracey's Pokémon eventually spot a badly injured Scyther, nearly passed out from exhaustion. Ash checks his Pokédex as Tracey steps forward to treat it. Scyther wakes up as Tracey tries to use a Potion, subsequently jumping back and assuming a battle position. However, it is too weak to fight, barely able to even stand. Ash throws a Poké Ball in an attempt to catch it, but Scyther swats it away, falling to its knees before struggling back up. Ash attempts to send out Pikachu, but Tracey steps in with his Venonat. Tracey orders a Sleep Powder attack, which puts Scyther to sleep despite its attempt to escape. Tracey tosses a Poké Ball, easily catching Scyther.
Meanwhile, Team Rocket is flying over the island in their balloon, surveying the land. A Beedrill flies towards them and cuts through the balloon, bringing it down. Team Rocket gets out of the wreckage and notices all of the Bug Pokémon around before stumbling across a Scyther swarm. The leader, denoted by two cuts forming a cross on its forehead, leads an attack on Team Rocket.
At the Pokémon Center, Nurse Joy and Chansey work on Scyther. Ash, Misty, and Tracey watch through the window as Scyther glares at Tracey (which Misty points out to the group), seemingly mad at being caught. Chansey brings Scyther out of the room and takes it to recovery. Joy concludes that it lost its swarm leadership position from battling a younger Scyther challenger. The loss forced it to leave the swarm and live in exile unless it wins another leadership match. Ash calls Professor Oak, who points out that Scyther's self-esteem is probably low due to losing its leadership and then being caught. Oak suggests that Tracey improve Scyther's mood and get it back in shape.
After outrunning the Scyther swarm, Meowth and James notify Jessie that her hair was crudely cut short. After checking it with her compact, she is outraged and declares her intent to confront the Scyther responsible. Meowth stops her and plans a method to capture the entire swarm. James also warns her if she gets exposed to their attacks, she could end up with a crew cut, much to Jessie's horror. Meanwhile, Tracey tries to help Scyther recover, but it is resistant. Ash remembers Scyther's love of battling and advises Tracey to help Scyther prepare for a rematch.
Team Rocket watches the Scyther swarm as they rest by a pond. Jessie fires a bazooka loaded with yellow glue into the air, which immobilizes the swarm, before Meowth nets them all. Scyther hears their cries and flies out of the Center, but it then crashes back to the earth, still weak. Tracey tries to stop Scyther, but it resists and flies away again. Tracey and his friends follow.
Tracey's Scyther finds the trapped swarm and cuts them loose before confronting Team Rocket. Ash and the others arrive, noticing Jessie's hair and quickly making fun of her. Furious, Jessie brings out Arbok and Lickitung, while James brings out Weezing and Victreebel. Ash sends out Pikachu as Weezing uses Smokescreen to cover the field. Scyther blows it away with Swords Dance, but it is still exhausted. Meowth translates that Scyther came back not to challenge the leader but to protect its brethren. Team Rocket's Pokémon outnumber Scyther four to one and Pikachu tries to step in, but Scyther wards him away. Ash tries to order Pikachu in, but Tracey stops him, saying Scyther needs to prove itself.
Meowth even joins the Pokémon to attack, leading the charge, but Scyther easily swats him away. Lickitung and Victreebel try to hit Scyther, but it flies up, and Victreebel bites Lickitung. Arbok attacks from underneath Scyther, but Scyther uses Double Team to throw Arbok off, sending it back to the ground. Scyther lands and tries to rest as Victreebel attacks with Razor Leaf. Scyther stops the attack with its scythes as Tracey reveals how he knew Victreebel would use the move. Arbok attacks with Poison Sting, but Scyther dodges. It then collapses, low on stamina and unable to dodge a second Poison Sting. The new leader steps forward and teams up with Tracey's Scyther. The leader launches Tracey's Scyther at Team Rocket's Pokémon, enabling it to attack them with Slash, defeating them all in one fell swoop. Angry and desperate, Jessie tries to fire a bazooka, but Pikachu stops her with Thunderbolt. Scyther attacks Team Rocket and leaves them with mohawks, causing them to retreat.
The Scyther swarm washes off the glue as the new leader and Tracey's Scyther give their respect to each other. The swarm departs as Scyther regains its confidence, joining Tracey. As he officially announces his catch, Ash tries to correct his style so it could resemble how Ash celebrates his catches, much to Misty and Pikachu's annoyance and Togepi's amusement.