Earl's Pokémon Academy
The trainer school of the Johto region is located within this city. In here, various tutorials and details of the game's mechanics are listed

Gym
The Violet City Gym is the first gym of the Johto region. This gym has no special puzzle in either game, but features paths which can allow you to skip the trainers until you reach the Gym Leader; Falkner. Earning the Zephyr Badge allows you to use HM06; Rock Smash outside of battle

The Ruins of Alph are a set of ruins located south-west of Violet City. These ruins have four different entrances in which to gain access to various Unown forms, two of which only accessible through Union Cave. There are a few hidden rooms which require you to use various moves or items which give even more items.

Kurt
Kurt dwells within this town and will exchange the Apricorns you find for specially made PokéBalls which cannot be found elsewhere.

Gym
The Azalea Town Gym is the second gym of the Johto region. This gym has you travel on various Spinarak platforms which travel across certain webs until you reach the Gym Leader; Bugsy. Earning the Hive Badge allows you to use HM01; Cut outside of battle

Gym
The Goldenrod City Gym is the third gym of the Johto region. This gym has you travel through a maze which matches the shape of Clefairy until you reach the Gym Leader; Whitney. Earning the Plain Badge allows you to use HM04; Strength outside of battle

Gym
The Ecruteak City Gym is the fourth gym of the Johto region. This gym has navigate a path using a small torch, defeating trainers as you go. However, if you fall off of the path, you are returned to the start. Continue until you reach the Gym Leader; Morty. Earning the Fog Badge allows you to use HM03; Surf outside of battle

Olivine City is a coastal city which contains the Glitter Lighthouse as well as a dock which takes you to Kanto on the SS Aqua. In this city, you can also obtain seals for your PokéBalls. Can't ride the SS Aqua until after you beat Johto Elite 4.

Gym
The Olivine City Gym is the sixth gym of the Johto region. This gym has no extra trainers and is only accessible after you have healed Amphy in the Glitter Lighthouse. Go up the path until you reach the Gym Leader; Jasmine. Earning the Mineral Badge allows you to use no extra move outside of battle. Later in the game, you can trade with Jasmine to get her Steelix

Gym
The Mahogany Town Gym is the sevent gym of the Johto region. This gym has you go through several rooms, completing various ice puzzles until you reach the Gym Leader; Pryce. Earning the Glacier Badge allows you to use HM05; Whirlpool outside of battle

The Lake of Rage is located at the northern point of Johto. This lake often has rain and changes its water depth depending on the day. On Wednesdays, the lake dries up, giving you access to various other parts of the lake. During the first time at the lake, a Shiny Gyarados, said to be forced to evolve by Team Rocket's radio messages, will dwell. You will only run into Shiny Gyarados if you win the badge in Mahogany Town and all the Badges before that. Will only catch it once

Move Relearner
The Move Relearner is found in the same building as the Move Deleter. The Move Relearner will teach your Pokémon moves in its level-up that it could have learned at lower levels. He charges you one Heart Scale per move.

Move Tutors
In the same house as the Move Deleter and Relearner are two move tutors who will teach moves to your Pokémon if they're of a high happniess. One will teach Draco Meteor to your Dragon-type Pokémon while the other will teach Frenzy Plant/Blast Burn/Hydro Cannon to various starter Pokémon.

Gym
The Blackthorn City Gym is the final gym of the Johto region. This gym has go through a path on platforms along some lava until you reach the Gym Leader; Clair. Upon defeating her, she will refuse to give you the badge until you get to the Dragon's Den