New Bark Town
This is the hometown of the player. You receive your starter Pokémon here from Professor Elm.
This is the second city that the player encounters. It is next to the sea and is full of flowers.
This is the third city that the player will encounter. It is in the center of Johto. In this city, the player can battle the first gym leader, Falkner. He is the Flying-type gym leader and defeating him will have you receive the Zephyr badge.
This is the fourth town that the player will encounter on his/her journey. This town has the Slowpoke Well where Slowpoke roam. It is in the eastern most part of Azalea Town. In this town, the player can challenge the gym leader, Bugsy. Defeating this Bug-type gym leader will award you with the Hive Badge.
This is the fourth city and the largest in Johto that the player will encounter. This city has the Radio tower that will have an event take place with Team Rocket taking over later in the plot. This city is home to one of the hardest gym leaders, Whitney. She is the normal type gym leader with a very strong Miltank. Defeating her will have you receive the Plain badge and make her cry 🙁
This is the fifth city that the player will encounter. This city has a historical tower named the Burned Tower. It is said that three unknown dogs were inside the tower while it was burning. These dogs transformed into the 3 mighty beasts: Entei, Raikou, and Suicune. You can encounter Ho-oh, Lugia, or Suicune (depending on your cover legendary) later in the plot. You can also battle the fourth gym leader, Morty. Morty is the Ghost-type gym leader and defeating him will have you earn the Fog Badge.
This is the sixth city (excluding passing Olivine City) , the player will encounter. This city is by the sea around the mountains. You also meet the Suicune Master here where he talks about wishing to meet Suicune (Spoiler, you do). After, You’ll be able to challenge the Fighting-type gym leader, Chuck. Once you defeat him, you receive the Storm Badge.
This is the seventh city that the player will encounter. This city is next to the sea and near the battle tower (Crystal only has battle tower). This city includes the lighthouse that is lit by Ampharos. After you complete the game, you will be able to access the boat that takes you to the Kanto Region. Jasmine is the Steel-type gym leader of Olivine City. Once you defeat her, you’ll receive the Mineral Badge.
This is the eighth town that the player will encounter. This town is one of the smallest towns and is known for a hiding place. In the story, the player encounters the champion of Johto, Lance. He leads the player into the Team Rocket hiding place. This town has the Ice-type gym leader, Pryce. Once you defeat him, you receive the Glacier Badge.
This is the ninth and final city in Johto that the player will encounter. This city is known for being a quiet mountain retreat. This is where you can battle the final gym leader, Clair. Clair is a Dragon-type gym leader and defeating her will have you receive the Rising Badge and qualify you for the Elite Four.