Ash, Misty, and Brock have all gotten completely lost trying to find the Fuchsia City gym, located in the middle of nowhere. They stop for a break, and let out a couple of their Pokémon out for a stretch. Misty tells Psyduck, who was drinking from a stream nearby, that cold water makes a headache worse, then comments that sometimes when she looks at him, she gets a headache as well. Misty offers Psyduck for Brock's Vulpix, but he declines. She retreats Psyduck and the three go on their way, with a Venonat secretly spying on them in the trees.
They carefully cross a bridge, and arrive at a Japanese style dwelling. The decide to look for someone there to ask for directions to the gym, and go in, with the Venonat still following them. Once inside, Ash and his friends cannot find anyone. Misty leans against a wall, and disappears. Brock inspects the wall, and declares it to be a secret door. He pounds on it, and it opens, revealing Misty inside. Suddenly, the Venonat appears. He runs off, and Ash and his friends follow him. Ash accidentally steps on a Voltorb in the floor, and is shocked. They all then dash up some stairs, and see the Venonat at the end of a hallway. Ash runs toward it, but runs smack into an invisible wall. They all decide to leave, and Ash slams into another wall. Brock voices his suspicion of that they have fallen into a trap. Brock hopes that whoever did it isn't wanting to steal their Pokémon, as he doesn't want to lose his Vulpix. Ash climbs up to look through a window, and the whole wall tips out over a deep valley. Brock and Misty think that he's dead, but soon find him hanging onto the wall for dear life. They pull him up and all agree at how dangerous the house is.
The other wall opens, and Ash and his friends see the Venonat again. Ash rushes through, to see several Ninja Stars flying at him. Misty and Brock go through, and find him pinned onto the panel. They hear a laugh behind them, and turn to see Iya, and Ninja Warrior. Ash yells at her for throwing the Stars around, and Misty agrees, asking Brock for support. Brock, however, is smitten, and he tries to make her acquaintance. She pushes him over in disgust, and informs them all that the house is a Ninja training camp. She tells them that the Venonat had told her of three stupid people who entered the house, and that she won't let them leave until she battles them. Ash accepts, and sends out Bulbasaur against Iya's Venonat. Bulbasaur uses tackle, but Venonat dodges and uses Stun Spore. Bulbasaur blows the dust away and uses Vine Whip, but Venonat dodges the attack again. Venonat uses Psybeam, and Bulbasaur gets confused, but shakes it off quickly. Bulbasaur uses Leech Seed, and finally connects, winning. A Voltorb rolls in, and explodes, filling the room with smoke. A voice is heard behind Iya, and scolds her for her ignorance. Iya apologizes, calling him her brother. Brock misinterprets the words, and tries to suck up to him, only to be bashed over the head with Misty's mallet. He tells them that he will not let Ash and his friends leave until they battle him. When Ash asks exactly who he is, he responds that he is Koga, the Fuschia Gym leader. Ash is surprised that it is the gym, but is glad that it is.
Outside, Team Rocket find the building. They plan to steal the poisonous Pokémon that Koga uses, saying that they would be perfect for Team Rocket's schemes. She tosses a rose to James, who pricks his finger. After he complains, Jessie throws her binoculars at him, and tells him to come inside. Back inside, Ash accepts Koga's challenge. Koga pulls out a Soul Badge telling Ash that he will win it if he wins. Ash assures him that he will. Ash sends out Pidgeotto, and Koga sends out Venonat. The Venonat immediately evolves into Venomoth, much to Ash's worry. Venomoth uses Stun Spore, and Pidegeotto's Whirlwind doesn't succeed in blowing the spores away. Venomoth then uses Sleep Powder, and Pidgeotto falls asleep. Ash then sends out Charmander, who succeeds in blocking Venomoth's Stun Spore with Flamethrower. Suddenly, the ceiling caves in. Team Rocket drops in, and does a rather dramatic and drawn out motto. Meowth tells Koga to hand over the poisonous Pokémon, but Ash tells him to go away. Jessie and James try to move, but can't very well due to the elaborate costumes they're wearing. They throw them off and send out Arbok and Weezing. Ash and Koga decide to join together and send out Charmander, Venomoth, and Venonat. Team Rocket throws some sort of webby stuff, and all three Pokémon can't move. Pikachu jumps out, but is wrapped up as well. Misty is about to send out Starmie, but Psyduck comes out instead. Psyduck proceeds to thoroughly annoy Misty. Ash has her use his Pokédex to find out what Psyduck's attacks are. After two very unsuccessful Tail Whip and Scratch attacks, Koga pulls a cord, and several Voltorb fall from the ceiling. Jessie and Meowth don't know what they are, and James fills them in. It's too late, though, and they explode. Ash, Koga, and the rest, along with there Pokémon run through a door, and into a strange room on a slant. They try to take off the webby stuff on their Pokémon, but to no avail.
Soon enough, Team Rocket bursts in. Meowth uses the slanted floor to their advantage, and rolls a Voltorb at Ash and his friends. It explodes, and when the dust settles, Psyduck is running around clutching his head. Misty tries to return him, but is unsuccessful. Meowth gets perturbed, and kicks Psyduck repeatedly. Psyduck's headache becomes worse, and he suddenly releases a Disability attack at Team Rocket, immobilizing them. Ash then uses Confusion, and sends Team Rocket flying into the air. The continuous energy released from Psyduck melts away the webbing on the other Pokémon and they are very happy. Dexter explains that Psyduck can use the attacks that he did when his headache gets severe.
Koga is grateful that Team Rocket is gone and is very impressed. He asks if Misty would like to trade for a Venonat or Venomoth, but Misty refuses, hugging Psyduck. Ash realizes that his match with Koga is still unfinished, and the group goes outside. Koga sends out Golbat to fight Ash's Charmander. Golbat disorients Charmander with a Screech attack, and he ends up accidentally scorching Brock with Flamethrower. He finally hits Golbat's wing, and Ash has him finish Golbat out with Fire Spin. Koga gives the Soul Badge to Ash, congratulating him. Ash, Misty, and Brock then continue on their way.