Ash, Misty, and Brock are journeying along, when they come to a very high cliff. Brock checks the map, then points to a ridge, saying that it will take them directly to Saffron City and another gym. Ash looks up in the sky and sees hundreds upon hundreds of Butterfree flying through the air. Ash wonders why they're there, and Brock explains that it is their mating season, when Butterfree get together to mate, fly over the ocean to lay eggs. Ash realizes that he'll have to let his Butterfree mate as well, or he will never have babies.
They rent a hot-air balloon and go up to view the happenings. Ash realizes his Butterfree, and he flies off into the crowd in search of a mate. He isn't doing all that well, and he comes back. Brock notices a beautiful girl release her Butterfree, and tells him to go mate with the new arrival. Butterfree looks confused, and Brock explains that if the two Butterfree get together and fall in love, possibly the two trainers can meet and fall in love too. Misty pounds him on the head and tells him not to mess with Pokémon love affairs. She then tells Butterfree to go ahead back into the crowd and search some more.
Butterfree flits around for a moment or two, then sees a pink Butterfree, instantly falling love. He begins his courtship dance, and Brock explains that if the other Butterfree feels the same way, she will do a dance as well. Unfortunately, she doesn't appear that she returns Ash's Butterfree's feelings and starts to fly off. Butterfree continues the dance, but gets a slap in the face. He is so depressed that he flies off, forcing Ash and his friends to land and look for him. They find him, and he looks extremely sad. Brock can feel for him, and announces that he could write a book on the secrets of love and heartache. Misty teases him and asks him if that would be his autobiography.
While Pikachu and Butterfree talk, Ash tries to figure out how to get the pink Butterfree to like his Butterfree. He suggests that Butterfree show off his moves, and Misty agrees saying that you need to be assertive in love. Brock asks if she means it and is upset that he didn't know this sooner. He then ties a little ribbon around Butterfree's neck, and everyone agrees that it's a nice touch. They then all go back into the air to search for the pink Butterfree that Ash's Butterfree so admired. They find her, and Butterfree struts his stuff, showing her his Whirlwind and Tackle attacks. It doesn't work, and Butterfree is heartbroken once again.
Suddenly, Team Rocket shows up in a helicopter and, after doing their motto, sweep up the Butterfree in a huge net. Ash, Misty, and Brock try to tell them to stop, but to no avail. They catch all the Butterfree, that is, except for Ash's. Ash's Butterfree tries to stop Team Rocket himself, but it doesn't work. Ash is about to send out Pidgeotto, but Misty stops him, saying that it would devastate Butterfree. Team Rocket flies off, with Butterfree soon behind. Ash and his friends follow in their balloon. They soon reach a canyon, and find Butterfree. He leads them to where Team Rocket has stashed the Butterfree. Inside Jessie, James, and Meowth are feeling pretty darn proud of themselves. Meowth imagines being "top cat" again and laughs loudly. Suddenly, a window breaks, and Ash and his friends climb in. Ash and his friends occupy Team Rocket, while Butterfree throws himself against the cage to free the other Butterfree. The pink Butterfree sees what he is doing and falls in love with him. Finally, Butterfree is able to break the cage, and all the other Butterfree fly out. Brock opens the doors, and they all fly outside, while Team Rocket tries to catch them again. James approaches the pink Butterfree, when Ash's Butterfree uses his tackle to knock him away.
Team Rocket takes off in the helicopter again in order to catch the Butterfree all over again, while Ash and his friends follow them in their balloon. Pikachu jumps on Ash's Butterfree's back and he flies him over to the helicopter. Pikachu jumps onto the windshield and Thundershocks the chopper, destroying it. Team Rocket falls into crevice and disappear. Butterfree flies back to the balloon and Pikachu jumps off. The pink Butterfree then flies up to Ash's Butterfree and does a little dance, signifying that she wants to be with him.
They all fly back to the cliff area to say goodbye as they need to fly across the ocean together. Ash tells the pink Butterfree to make sure she takes good care of his Butterfree. She nods and flies up into the air. Butterfree is sad to leave Ash, and he is too. As the Butterfree start to fly away, Pikachu tearfully waves goodbye, and Ash remembers his life with his Butterfree. He thinks of everything from when he was his first catch ever as a Caterpie, to when he evolved into Metapod, then Butterfree, to when he battled Misty for the Cascade Badge with him. He breaks out of it just as Butterfree starts to fly out into the distance. Brock then tells him that he raised Butterfree to have a lot of courage and that Ash has a lot of courage himself.