After his victory in the Orange Islands, Ash, Misty, and Tracey return to Pallet Town. Here, they reunite with Brock, who has given up being an assistant for Professor Ivy. Tracey decides to stay in Pallet Town in order to work with his idol, Professor Oak. Ash, Brock, and Misty continue on their Pokemon journey by heading to the Johto region.
During his time in the Johto region, Ash acquires several new Pokemon: Heracross, Chikorita (which evolves into Bayleef), Cyndaquil (which evolves into Quilava), Totodile, Noctowl, and Phanpy (which evolves into Donphan). He, along with Misty and Brock, meet new trainers and become friends with many of them.
During his time in the Johto region, Ash also battles several Gym leaders to earn the eight badges he needs: Falkner (the Violet City Gym Leader), Bugsy (the Azalea City Gym Leader), Whitney (the Goldenrod City Gym Leader), Morty (the Ecruteak City Gym Leader), Chuck (the Cianwood Gym Leader), Jasmine (the Olivine City Gym Leader), Pryce (the Mahogany Town Gym Leader), and Clair (the Blackthorn City Gym Leader).
After earning all eight badges that he needs, Ash competes in the Silver Conference. He makes it through all the qualifying matches, and becomes one of the competitors in the Victory Tournament. Ash makes it into the Top 8, and even beats his long-time rival, Gary Oak. However, Ash ends up being defeated by a trainer named Harrison from the Hoenn region.
After the Silver Conference, Ash decides that after a brief visit to Pallet Town, he will continue on his Pokemon journey by going on to the Hoenn region. Before they make it to Pallet Town, Misty receives a message from her sisters; they ask her to return to the Cerulean Gym and take over the gym leader duties. At that point, Brock decides that he needs to return home to Pewter City to help his father take care of Brock's brothers and sisters. So Ash returns back home on his own to get ready for his upcoming journey to the Hoenn region.
| The Johto Journeys | 41 | 1999-2000 | Norihiko Sudo | Shogakukan Productions Co., Ltd./SoftX | 4 Kids Entertainment |
| Pokemon 3: The Movie | N/A | 2000 | Kunihiko Yuyama | OLM, Inc. | 4 Kids Entertainment/Warner Bros. |
| Mewtwo Returns | N/A | 2000 | Kunihiko Yuyama | ? | 4 Kids Entertainment/Warner Bros. |
| Johto League Champions | 52 | 2000-2001 | Norihiko Sudo | Shogakukan Productions Co., Ltd./SoftX | 4 Kids Entertainment |
| Pokemon 4Ever | N/A | 2001 | Kunihiko Yuyama | OLM, Inc. | 4 Kids Entertainment/Miramax |
| Master Quest | 65 | 2001-2002 | Norihiko Sudo | Shogakukan Productions Co., Ltd./SoftX | 4 Kids Entertainment |
| Pokemon Heroes | N/A | 2002 | Kunihiko Yuyama | OLM, Inc. | 4 Kids Entertainment/Miramax |
