Ash and the gang begin to head back through Granite Cave so Ash can have a re-match with Brawly. Along the way, Corphish startles the same Loudred that the group ran into before. While fleeing from the Loudred, Ash, Brock, Max, and May get separated from their Pokémon. Pikachu, Silcoon, Corphish, Treecko, Mudkip, Torchic, and Lotad end up falling into a river and landing at the bottom of a waterfall. Treecko and Corphish almost get in a fight, but are stopped by Mudkip and Pikachu. The Pokémon set off to find their owners.
Throughout all this, Team Rocket ends up lost in the same cave and startles the same Loudred, which sends them blasting off again. While the Pokémon are trying to find their way back, they encounter a mischievous Nuzleaf. Corphish slashes its leaf and Nuzleaf retaliates by making a very loud noise. The Pokémon soon find out that the Nuzleaf was actually calling its friends who slowly capture and cage all the Pokémon except for Pikachu and Mudkip. Pikachu and Mudkip try to reason with the Nuzleaf group, but to no avail. Team Rocket appears again and, after observing all this, decides to capture all the Pokémon, including the Nuzleaf.
Meanwhile, Taillow is searching for the lost Pokémon and reports back to Ash and the gang when it sees them. Team Rocket captures the Pokémon using their balloon, but Ash and everyone arrive just in time to thwart their plans. Ash rescues the Nuzleaf group, who then hold a net for Ash to fall into from the balloon. Team Rocket is sent on their way by Corphish and Treecko teaming up. The episode ends with all the Pokémon happily playing with one another and their new Nuzleaf friends.
Following a morning full of training, Ash, his friends and their Pokémon begin making their way back to camp thorough a cave. Max asks Brock to make some special stew for breakfast, but Brock says he will only if Max would make a funny Corphish impression, which he does and makes everyone laugh. Meanwhile, Corphish goes into a tunnel and discovers a Loudred sleeping. Corphish tries poking Loudred before pinches its ear with its pincer. Loudred instantly wakes up from the pain. As it begins to rushes around the cave, it screams loudly, hurting everyone's ears in the process. Brock sends out Forretress, who uses Rapid Spin on a wall to create an escape route. As they call for everyone to escape, Silcoon rolls out of May's hands and Pikachu, Torchic, Lotad, Mudkip, Corphish, and Treecko follow it. Loudred burrows underground while the group notice all of their Pokémon are missing.
Pikachu soon locates Silcoon on a ledge overlooking a river. Corphish reaches over to grab Silcoon, but it instead slips from Corphish's claw and into the water below. All the Pokémon dive in, and Pikachu grabs a hold Silcoon with his hands as they approach a waterfall. They all fear the worst, but are relieved when they land in a forest area. Pikachu looks around to see if everybody's okay, but Corphish is stuck in a hole! Treecko knocks Corphish out of the hole and makes it fly into the air, landing with a thump, making Corphish very angry. Pikachu and Mudkip quickly intervene to stop the fight. Suddenly, Torchic begins crying, missing May, but Pikachu soon calms it down. Pikachu and Mudkip pick up Silcoon and walk off, with the other Pokémon following not far behind. Meanwhile, after searching the whole cave, Ash and the others decide that the Pokémon somehow got out. May is worried about Torchic running into a scary Pokémon. Max says that the Pokémon they saw was a Loudred and Ash looks it up in his Pokédex. Everybody heads outside to continue to search for the Pokémon. Ash tells his Taillow to search for the Pokémon.
Later, Team Rocket enters into the cave looking for the twerps. James suggests they must have lost track of them. Jessie is unimpressed and scolds James for not bring a flashlight along, which leads to an argument over the responsibility. Wobbuffet pops out of his Poké Ball, standing directly on Loudred. Jessie tells him to get off of it but before Wobbuffet can, Loudred wakes up and begins to storm around the cave, blasting Team Rocket off.
Meanwhile, the Pokémon are all walking when Corphish stops to eat a mushroom. Pikachu runs over and knocks it out of its hands. Pikachu tells Corphish that the mushrooms are poisonous. Mudkip finds some Berries for Corphish to eat, but Corphish eats them to fast and begins choking on one. Treecko hits Corphish and it stops choking. The Pokémon begin to walk again as a Nuzleaf watches them from a tree. Nuzleaf plays a song on a leaf which causes all of the Pokémon to become drowsy. Nuzleaf laughs as they walk around in circles. Treecko realizes something is amiss and alerts Pikachu to the dilemma. Nuzleaf hops out of the tree and Corphish rushes in to attack it. Nuzleaf leaps back to evade, but it is alarmed to see that Corphish has cut the leaf on its head, causing the Pokémon to laugh. Nuzleaf calls its friends over and runs off. In spite of the threatening echoes of Nuzleaf, Pikachu is determined not to let anything happen to the other Pokémon. As the Pokémon continue to walk, they begin to get picked off. Corphish is captured after it grabs some Berries that are hanging down. Lotad disappears after it goes to swim in a pond. Treecko notices the other Pokémon are missing before being pulled into the trees by its tail. Torchic becomes distracted by some flowers before being picked off. As Pikachu and Mudkip are walking, Silcoon is grabbed from them. They notice two Nuzleaf above them and follow them as they run off. Ash's Taillow sees them running and flies back to report the news to Ash and his friends.
The nabbed Pokémon are all kept in a big cage by the Nuzleaf as a raging bonfire burns. Treecko and Corphish both try to break the cage, but to no avail. Team Rocket spies on the scene from the nearby bushes, and Meowth reveals that the Nuzleaf are considering burning the Pokémon at the stake because Corphish damaged the leaf on one of the Nuzleaf's heads. Jessie admits that if anything happened to her hair that Nuzleaf's course of action is reasonable. As Pikachu and Mudkip rush in, the Rocket trio set their sights on stealing all of the Pokémon and the wild Nuzleaf. Pikachu is prepared to shock the Nuzleaf, but Mudkip settles on negotiating with them. The Nuzleaf are uninterested in Mudkip's suggestion before Team Rocket nabs the Nuzleaf in a net and Pikachu with a rubber hand. Team Rocket ask the Pokémon to prepare for a trouble and they recite their motto. Pikachu uses Thunderbolt but it has no effect, neither does the Nuzleaf's attacks. Mudkip runs over to the cage and uses Water Gun on it. Their Trainers appear and Taillow and Forretress use Quick Attack and Rapid Spin respectively on the cage to break it. Ash has Corphish use Crabhammer on him to launch himself up to the balloon to free the Pokémon. Team Rocket laughs as Ash attempts to untie the net. Ash manages to get it untied and releases the Nuzleaf who jump to the ground. As he gets to work on Pikachu, James has Cacnea use Pin Missile on Ash, but it misses and instead strikes the claw allowing for Pikachu to be freed. Brock says he is worried that Ash and Pikachu will get hurt if they jump down from that height. Brock spies the net and calls over the Nuzleaf to help them hold up the net before Ash and Pikachu jump onto it. Treecko launches Corphish with its tail. An airborne Corphish uses Bubble Beam on the balloon and blasts Team Rocket off. Treecko then catches Corphish as it lands back on the ground, creating a truce between them. Afterwards, the Trainers are pleased as they watch their Pokémon and the Nuzleaf now getting along.