Ash, Misty, and Brock are walking through a forest when they notice a bird house up in a tree. They wonder which Pokémon could go there when a Noctowl appears, and they hide so that it won't be scared off. Ash looks it up on his Pokédex. A man then shoos the Noctowl away by using a branch from where he is hiding on the tree, saying that this Noctowl isn't the one he wants. The Noctowl flies away. A rare, Shiny Noctowl then appears outside the bird house. The man takes out a stick with berries and moves them up at the Shiny Noctowl. However, the Noctowl kicks the berries away; hits the tree, causing the man to barely hang onto a branch; and pecks at the man's fingers, causing him to fall to the ground.
The group approaches the man and asks if he is alright. The man then introduces himself as Dr. Wiseman and says that he wants to catch the Shiny Noctowl but it keeps outsmarting him. The Shiny Noctowl is smaller and cleverer than the average Noctowl, making it even rarer, which is why Dr. Wiseman wants it. Ash decides that he wants to catch that Noctowl, and throws a Poké Ball at it, but it kicks the Poké Ball right back at Ash. The Noctowl uses Hypnosis on Ash, causing Ash to think that a rock is his Pikachu. Ash picks up the rock but falls on his back with the rock on top of him, and Noctowl flies away. In Dr. Wiseman's cabin in the forest, Dr. Wiseman tells the group that he is only interested in catching the rarest and most unusual Pokémon. Misty says that she has a rare Pokémon and calls out Psyduck. She explains that her Psyduck is rare and unusual because it can't fly or swim. Dr. Wiseman is even more determined to catch the Noctowl as he hears Misty laughing, because laughter reminds him of the way Noctowl mocks him. Dr. Wiseman vows that he will outsmart the Noctowl, as does Ash. Dr. Wiseman has a secret trap to catch the Noctowl. Ash wants to see it, but Dr. Wiseman doesn't let him. Ash says that he won't use traps and will catch the Noctowl fair and square. Team Rocket overhears them while they are on the roof and plans to give the Noctowl to their Boss.
Dr. Wiseman is seen sitting on a branch and setting his trap, while Ash, Misty, and Brock watch him behind bushes. Dr. Wiseman joins the group as Noctowl lands on the branch. Dr. Wiseman pulls a rope which reveals a mirror next to where the Noctowl stands. Noctowl sees its reflection and uses Hypnosis on its reflection which makes the Noctowl hypnotize itself as the mirror reflects the move back. Noctowl falls out the tree after hypnotizing Dr. Wiseman who picks up a rock, believing it to be the Noctowl. Noctowl is seen wobbling away as it is still under Hypnosis. Ash asks Noctowl whether it is okay. Noctowl turns around and Brock warns Ash that Noctowl might feel threatened by him. The wind picks up and a branch hits Dr. Wiseman, which makes him realize he is holding a rock. The wind turns out to be caused by a massive regular-colored Noctowl machine controlled by Team Rocket. Meowth breaks the fourth wall by saying they are going to capture the Shiny Noctowl after the commercials.
Pikachu uses Thunderbolt to hit the machine, but the attack bounces back at the group. Ash calls out Totodile and Cyndaquil. Team Rocket blow up the balloons on their machine, blowing Cyndaquil and Totodile away. Dr. Wiseman decides to catch the Noctowl while everyone is distracted by the wind. Team Rocket notice him running away and carrying Noctowl with him, so they grab him with a mechanical Noctowl foot. Dr. Wiseman is flung away as the robot catches the Noctowl. Team Rocket celebrate as they begin to fly away. Ash, not giving up, sends out Bulbasaur and Chikorita who use Vine Whip to stop the robot Noctowl from flying away. Ash climbs a tree to get to the Shiny Noctowl. Ash jumps onto the mechanical Noctowl foot and tries to pry the foot open. Psyduck tries to use Confusion but it turns red and falls down. Ash manages to loosen the mechanical foot just enough so that Noctowl can fly away. Ash falls through the trees and Noctowl talks to Ash's Pokémon. Cyndaquil uses Flamethrower on the robot, and then Totodile takes over by using Water Gun while the robot is boiling hot. The metal begins to crack. Pikachu uses Thunderbolt in the crack formed, causing the machine to blow up and blasting off Team Rocket.
Noctowl challenges Ash to a battle. Dr. Wiseman decides that it's too smart for him so Ash should try to catch it. Ash uses Pikachu to fight against Noctowl. Pikachu uses Thunderbolt while Noctowl uses Hypnosis. Pikachu becomes confused and sends the Thunderbolt everywhere, even hitting himself and making himself go back to normal. Pikachu runs away as Noctowl flies close behind him. Pikachu listens to Noctowl's wings instead of looking at its eyes so that he won't get hypnotized. Pikachu successfully hits Noctowl with Thunderbolt and Ash throws a Poké Ball at Noctowl, catching it. The episode ends as Ash and his friends bid farewell to Dr. Wiseman while continuing towards Goldenrod City.