With three badges down, Ash and the gang's next stop is the gym in Saffron City. But first, they decide to take a cruise on the Saint Anne, where trainers cruise for free. Unknown to the trainers, the cruise is a trap set by Team Rocket.
While moving on his journey, Ash feels a need to catch a new Pokémon. But while trying to catch Hitmonchan they meet a girl named Rebecca who asks for their help to get her father back. To help, Ash uses his Primeape against her father in a fighting Pokemon tournament. Will he win?
The group arrives in Gunjo City where everything is dark and gloomy. A Coil follows Pikachu everywhere ever since he caught a peculiar illness, but it is the Betobeta and Betobeton that are causing trouble in a local Power Plant.
Satoshi finds himself among a group of Pokémon Trainers hired to protect a construction site from the interfering ground Pokémon, Digda. The construction is shut down after it is revealed that the Digda and Dugtrio are trying to protect their home. Musashi's Arbo and Kojiro's Dogas evolve into Arbok and Matadogas respectively.
During a storm, Satoshi and his friends arrive at a mysterious Mansion. While there, Satoshi meets Imite, a girl who is an expert at impersonation, and she happens to own Metamon, a Pokémon that can transform into any Pokémon. However, Metamon cannot seem to figure out how to change its face, a fact that stopped Imite's variety show. As they all try to help Metamon perfect its transformation, the Rocket-Dan tries to steal the Metamon so it can transform into a Miniryu which they can give to the boss.
The group come into a forest where it is quiet and peaceful. They notice a large group of Pikachu that Satoshi's Pikachu tries to make friends with. After saving a young Pikachu from drowning and rescuing the herd from the Rocket-Dan, Satoshi's Pikachu is welcomed among the other Pikachu as one of their own. Saddened by this sudden distance, Satoshi tries to leave Pikachu behind (to Kasumi and Takeshi's shock and dismay), thinking that in the long run, it is going to be better off with its own kind. As they attempt to leave the forest with Satohshi still standing his ...
Ash and the gang come to a village where there is no food, because the river is dry and plants can't grow. They decide to investigate the problem and discover that the water is being blocked by a sleeping Snorlax.
When at a carnival, Satoshi and his friends meet a magician who is really losing his touch and fails in his own magic show. In his effort to get better, he decides to hypnotize Satoshi and uses his Pokémon Tamatama to capture loads of Nassy. But the Nassy end up hypnotizing themselves and the Rocket-Dan and almost destroy the entire carnival. Luckily, they are saved by Hitokage, who evolves into a disobedient Lizardo.
Having run out of medicine, Satohsi and his friends go to a local shop to get some Potions. However, they don't have much due to the owner's Paras being weak. Satoshi and his friends decide to help out the owner by training her Paras, hoping that it can evolve into Parasect.
Entering Neon Town, a bustling Metropolis where everyone is tired and rude, Satoshi and his friends find a Purin who is too shy to sing its hypnotic song. Realizing they can kill two birds with one stone, Kasumi tries to teach the Purin to sing while the Rocket-Dan attempts to record the song so they can use it against Satoshi. Everyone falls asleep, including Satoshi and his friends and the Rocket-Dan, and a miffed Purin uses the marker hidden in her microphone to draw on everyone's sleeping faces.
After Pikachu gets an apple stuck in its throat, Satoshi and his friends rush it to a Pokemon Center. After being treated, they hear of a traffic accident (caused by Rocket Dan) that has left many Pokemon injured. Satoshi and the gang are recruited to help treat all the Pokemon that cant fit in the Pokemon Center.
After finding a missing person sign featuring Kojiro, Satoshi and his friends decide to find Kojiro and inform him of his parents' death. However Kojiro's parents turn out to be alive, and their death was only a decoy to get him to return home to the rich Rumika, a girl Kojiro was arranged to marry from when he was a little child. Kojiro has left because Rumika is terrifying, so everyone tries to save Kojiro from this fate, including Kojiro' old pet Gardie, Gar-chan.
When Satoshi and his friends see a group of Gardie training against a Policeman posing as a robber, Satoshi decides for him and Pikachu to do the same training to become the best they can be. However, when the Rocket-Dan comes to steal them, Officer Junsa, Satoshi and the gang's voice gets changed, causing the Gardie to think that the Rocket-Dan are the Officers as they use their ears to follow command.