Ash, Misty, and Brock are reunited once again on a brand new journey. They venture west of Pallet Town into the region of Johto, where new adventures and Pokemon await them at every turn. They arrive in New Bark Town where Ash registers for the Johto League. However, they soon become involved in a rescue mission when Team Rocket breaks into Professor Elm's lab, and steal a Totodile.
Ash, Misty, and Brock start their journey to the first Johto Gym in Violet City. On the way they meet Casey, a brand new trainer who has just received her first Pokemon, Chikorita, from Professor Elm a few days earlier. She insists on a battle with Ash. Ash is hesitant since he is far more experienced then her, but eventually agrees. Ash picks Charizard, and easily defeats all of Casey's pokemon. She becomes discouraged and runs away crying. She then encounters Team Rocket who convince her that Ash cheated, and that they will help her win the right way. She agrees and goes to find Ash.
On the way to Violet City, Ash and friends come across a forest where Pinsir and Heracross are normally separated by a river into their own sections of the forest. However, something has happened in Pinsir's side of the forest, causing them to migrate to the Heracross part of the forest and stir up trouble. Ash and friends, along with a forest ranger named Woodrow and a friendly Heracross set out to find out why the Pinsir are leaving their part of the forest.
Ash and friends stumble across a valley where a girl named Rochelle uses Donphan to harvest Amberite, a gemstone only found in this valley. Ash, Misty, and Brock follow her as she makes her rounds, and see exactly how she finds it. However, Team Rocket hears about the gemstone and decides to steal a Donphan so that they can find their own Amberite.
Continuing their way to Violet City, Ash and friends have become lost in a forest. The forest seems to be haunted as the trees begin to move and faces appear on them. They try to run, but trees appear everywhere. Then a Hoothoot appears and uses Foresight to clear up the illusions. Gary appears and taunts Ash about going through the forest without a Hoothoot. Ash, Misty, and Brock go to rent a Hoothoot, and get stuck with one that is scared, can't use Foresight, and does not listen to Ash (but loves Misty). A series of crazy adventures ensues as they try to make it through the forest.
Upon finally making their way out of the forest, Ash, Misty and Brock find themselves at the outskirts of a large city called Florando. Wondering what they should do next, Misty suggests that they relax and do some sight seeing. Brock quickly jumps in and tells Misty that he cannot relax in a city full of girls that need his protection. As Ash, Misty and Brock walk along the city streets, they stumble across a young lady who advises them to see the Pokemon Exhibition. There they meet a girl named Bailey and her Bellossom. One of her Bellossom is not dancing properly, and Ash, Misty, and Brock decide to help her.
Our heroes make their way to Catallia City, a town recognized for its magnificent buildings. A patrol car barrels down the street, and knowing that Officer Jenny must be inside, Brock gives chase. However, a few seconds later, he trips over a thin web. Ash and Misty catch up with him and after Togepi notices something approaching, a Spinarak appears. Officer Jenny appears and tells them how in Catallia City they use Spinarak to help them. Ash, Misty, and Brock then become involved in a plot to stop thieves who are copying the legendary Black Arachnid.
Ash, Misty, and Brock arrive in the rich town of Palm Hills. At one mansion they notice butlers looking for something. The mansion's owner, Madame Muchmoney, is trying to find her Snubbull. Snubbull eventually appears. Madame Muchmoney invites them inside for lunch, where they discover that despite spoiling it, Snubbull doesn't want any of it. Madame Muchmoney is also planning for Snubbull to get married, and so it runs away again, and now everyone must find it before Team Rocket takes it.
In a city park, Ash and friends encounter a lost baby Stantler. Brock decides to help nurse it back to health and then release it back to the wild, but Team Rocket is planning on taking the young pokemon.
Ash encounters a wild Chikorita and begins to battle it, wanting to add it to his team. However, after battling Charizard, Chikorita is injured. Ash takes it to the Pokemon Center to get healed, but Team Rocket is disguise steal it. Ash chases after Team Rocket, trying to make sure the Chikorita is safe and unharmed.
Ash and friends arrive in Cherrygrove City where they have an encounter with a Quagsire. It steals the GS Ball and runs away. Officer Jenny tells them that the Quagsire do this every year on the night of the blue moon. Not wanting to wait for the GS Ball to float back down the river, Ash, Misty, and Brock follow the Quagsire up the river.
On the way to Violet City, Ash and friends meet Arielle, a trainer who owns a flock of Ledyba, and uses them to pollinate nearby trees. When Team Rocket steal some of the Ledyba (with some accidental help from Pikachu), Ash and friends must help Arielle find them before Team Rocket can get to far.
Team Rocket can't believe their luck when the Blissey employed in a Pokémon Center willingly gives them the center's entire food supply. As they abscond with the grub, however, an collective pang of conscience tells them to return their ill-gotten booty. However, they are ashamed lest this act of decency ruin their carefully cultivated reputation as troublemakers.
Ash, Misty, and Brock finally arrive in Violet City, the location the first Johto Gym. They come across a Pokemon Academy. At the academy a young boy named Zackie becomes obsessed with Ash's Pikachu and decides to catch it, even if it belongs to another trainer. However, he ends up catching a Bellsprout instead. Meanwhile, the rest of the class goes on a field trip to the Sprout Tower, where Team Rocket is waiting for Ash so they can get Pikachu.
Ash, Misty, and Brock finally arrive at the Violet City Gym, ready to face the Gym Leader. After a little tussle with Team Rocket, Ash challenges Falkner, the Gym Leader to a three on three battle in order to win his first Johto Badge.
Fresh off his win at the Violet City Gym, Ash and friends encounter a Marill that cries at everything. Following an encounter with Team Rocket, Misty, Togepi, and Marill become separated from everyone after being washed away in a river. Now Misty must somehow get back to Ash and the others while at the same time passing all of the many challenges of a forest.
Team Rocket's most recent super vehicle, the Arbotank, is their ticket to capturing Pikachu. That is until Togepi and its new found Sentret buddy climb inside and and end up taking it on a joyride. Now Ash. Misty, Brock, and Team Rocket must team up in order to stop the Arbotank and get Togepi back.
Ash and friends meet a girl named Liza, the person who protects the nearby Charicific Valley, a valley where wild Charizard live. Everyone goes there and Ash wants his Charizard to train with the others, but after it is easily beaten by another one, it loses its fighting spirit. Now Ash must figure out what is the best thing to do for Charizard.
Ash and friends arrive in Bloomingvale the day before the Annual Sunflora Contest. The meet a girl named Sonrisa who can not get her star Sunflora to compete. As the day of the contest arrives, will she be able to compete, especially when Team Rocket plans to steal all the Sunflora?
During a tough Pokemon Battle, Ash tries to call back Chikorita in order to use Pikachu, but Chikorita refuses to go back. Ash continues to try, but eventually the boy has to leave. At the Pokemon Center, Professor Oak and Nurse Joy tell Ash that Chikorita is probably jealous of Pikachu. That night Chikorita sneaks out of the Pokemon Center and Pikachu follows, but what will happen to the two?
Ash and friends come across a girl name Mariah and her pokemon Hoppip. Mariah uses her pokemon to forecast the weather. A brutal storm is heading their way and they must take cover before anything bad happens, but that's not so easy with the all of the pokemon that they must keep safe.
Ash and friends arrive in a town where there is a local superhero - Gligarman. However, upon meeting him, they realize that he is getting a little too old to be fighting crime by himself. He tries to get Ash to be his sidekick, but Ash refuses. Gligarman then faces a real big threat when Team Rocket show up with their newest machine.
Ash and friends meet up with Mary, a young girl who helps her parents operate a Mareep farm. She wants to enter the tournament in the upcoming Mareep Festival, but her mother does not want her to because she thinks she is not ready. Mary sets out to prove that she is ready for it and Ash, Misty, and Brock decide to help her.
When the most promising trainee at a Pokemon Dojo abandons battle altogether, opting to gather information for his comprehensive Poke-database instead, it's up to Ash and friends to convince him that battling, and life for that matter, is more than just a matter of probability.
Continuing their way to Azalea Town, Ash and friends come across a trainer who is looking for a Cyndaquil. According to rumors, there are suppose to be many of them living in the area. Ash gets excited and goes looking for one so he can capture it. However, the trainer from before is not to happen with this and capturing Cyndaquil turns into a contest between the two trainers.
Ash and friends finally arrive in Azalea Town. The town is currently in the middle of a drought. While walking through town Ash accidentally steps on a Slowpoke's tail, which causes the towns residents to chase after him, angry that he injured their mascot. They are saved by a man, who just happens to the be the Pokeball expert Kurt! Before they can deliver the GS Ball to him, they decide to help him investigate the cause of the drought.
Ash, Misty, and Brock arrive at Kurt's house and finally deliver the GS Ball to him. As he needs time to study it, they must find something to do. Since the gym is still closed, they decide to watch Kurt work and create Pokeballs. He makes them out of Apricorns, a special type of fruit that only grows in the Johto region. Kurt gives them each their own Fast Ball. He says he will make them more if they go and pick more Apricorn. As he only has a White Apricorn tree in his yard, his granddaughter Maisy takes them into the mountains outside of town to pick all different kinds of Apricorns. However, Team Rocket is not far behind and they want the Apricorns for themselves.
Ash and friends have delivered the GS Ball safely to Kurt and are heading to the Azalea Town Gym for the next badge. Misty thinks Ash will have a tough time without Charizard but Ash is confident that Cyndaquil has the firepower he needs. They arrive at the gym are are surprised to find out that it is a forest inside of a dome. The Gym Leader, Bugsy, appears and accepts Ash's battle. Bugsy specializes in Bug-Types, and quickly proves that Ash will need to think quickly if he is to earn his Second Badge.
Ash and friends find themselves inside the Ilex Forest. The encounter a young trainer named Sylvester who is having trouble with his Farfecth'd and can't get it to help him make Charcoal. Team Rocket appear and steal the pokemon, and now Ash, Misty, and Brock must help Sylvester get it back, and prove to Farfetch'd that he really cares for it.
Ash and friends arrive in a town where the Pokemon Swap Meet is being held. The event has many festivities, but the main one is where people trade their pokemon to other trainers. They meet a trainer named Benny who is trying to find someone to trade his Wobbuffet to. Ash, Misty, and Brock decide to help him find someone to trade to. Meanwhile, Team Rocket is using the event to trick trainers into giving them their pokemon. However, a run-in with the Magikarp Salesman leads to events that may change the outcome of Team Rocket's plans.
Ash and friends arrive in a new town where an event called the Fire and Rescue Grand Prix in going to be held. It is a firefighter competition, mainly for Water Pokemon. They are quickly reunited with two sets of old friends. First they meet Captain Aidan and Team Wartortle from the Orange Islands, and then they meet the Squirtle Squad. Both team are going to be in the competition. However, the Squirtle Squad have become essentially lost without their leader. In order to settle its rivalry with Team Wartortle, Ash's Squirtle rejoins the Squirtle Squad for the competition, and the end result will change everyone.
Ash and friends come across a school where a girl named Olesia takes care of some Wooper. She needs to run and visit her mother, but she can't take the Wooper with her. Ash, Misty, and Brock agree to watch them for her, but it turns out to be more then they bargained for.
Ash and friends come across a tunnel that is a shortcut to Goldenrod City. However, the Onix in the tunnel don't want to let anyone pass. Now they must find a way through the tunnel, but things are made worse when both Jigglypuff and Snubbull show up!
A group of wild Houndour is stealing stuff from people in town and terrorizing people in the forest, and people are becoming scared of them. But when one of them is attacked by a wild Golem, Ash and friends befriend them and make the long trek back to town to help the poor Houndour.
Ash and Misty's "friendly" rivalry is tested when they both try to capture a Totodile at the same time. Unable to determine whose Pokeball had captured the wild Pokemon, the two must battle it out to determine who gets Totodile.
When Ash and friends hear of a unbeatable trainer operating nearby, they seek her out. They are quickly stunned when both Brock's Vuplix and Ash's Cyndaquil are easily defeated by her Skarmory, despite having a huge type advantage. Ash then sets out to train Cyndaquil and help it with its flame problem.
Ash's Totodile falls head over tail for a passing Azumarill, but Azumarill doesn't care about it and sends it flying. Trixie, Azumarill's trainer comes along and says that she is trying to figure out why Azumarill is acting so strange lately. When Team Rocket kidnaps Azumarill, Totodile sets out to rescue and win the her love.
While walking through a forest on the way to Goldenrod City, Ash and friends encounter a rare Noctowl that is smaller then other Noctowl and has different colors too. This Noctowl is a trickster, and when Ash hears this he sets out to capture the tricky Pokemon.
When Molly Hale's sadness of her father's disappearance gets to her, she unknowingly uses the Unown to create her own dream world along with Entei, who she believes to be her father. When Entei kidnaps Delia, Ash, Misty & Brock invade the mansion looking for her and to try to save Molly from the fantasies of her dream world.
Ash and friends are wandering through a forest that is supposedly haunted by ghosts. Luckily they run into a girl named Cherry, who owns a Girafarig. Once they get to town, Ash decides to have a battle with this unique pokemon. Meanwhile, Team Rocket is planning on stealing all of the psychic pokemon in the town.
A Pokemon Fortune Telling boom turns out to be a Team Rocket plot to steal Pokemon from local trainers. The engineers of this plot, though, are not the Team Rocket regulars, but by the formidable Butch and Cassidy. Now it is up to Ash and friends to stop them.