Pokémon Crystal Version/Plot

The player is called to Professor Elm's lab to run an errand. He provides the player with one of three Pokémon:, , or to help him/her get to Mr. Pokémon's house. He/She meets Kanto's own Professor Oak during the errand for Elm. Oak, convinced that the player has started his/her own Pokémon journey, gives him/her a Pokédex. On the way back, the player is attacked by a spiteful and. Upon his/her return to New Bark Town, the player is informed that someone has broken into Professor Elm's lab and has stolen a Pokémon, the same Pokémon that the Trainer from earlier battled with (the Pokémon that the player's starter is weak against); even more so, that very same Trainer fits the description of the Pokémon thief. This Trainer will become the player's rival for the course of the game, having several conflicts with the player as to what it means to be the world's greatest Pokémon Trainer.

Team Rocket has returned with a new attitude, since the disappearance of their leader Giovanni, and once again tries to take over the world, starting with the Johto region. They begin with petty things (such as cutting off the tails of to sell as food for a high price) before becoming more devious, such as a plan to use radio frequencies to artificially induce evolution in some Pokémon at the Lake of Rage near Mahogany town. When the player defeats or captures the Red rampaging in the lake, Lance will arrive and congratulate the player for his/her battling and requests that the player help him find the source of the radio signals. When the player returns to Mahogany town and enters the Souvenir Shop, he/she will find Lance and his threatening the man in the shop. A secret door will open to the Rocket base, which was revealed by a Rocket Grunt to be an old ninja hideout. After the player defeats the Rocket Executive found in the hideout, Lance asks the player to help him knock out the Electrode powering the machine producing the radio waves.

After completing this task, Lance thanks the player and gives him/her the HM. After the player defeats Pryce - the leader of Mahogany Gym - Professor Elm will call the player and tell him/her about unusual broadcasts from the Radio Tower in Goldenrod City. When the player reaches Goldenrod City, it is revealed that Team Rocket has taken over the Radio Tower, their intent being to try to contact their missing leader, Giovanni, and persuade him to return to Team Rocket. Also, the Director of the Goldenrod station has been kidnapped and replaced by an impostor. After the player defeats the impostor, he will tell him/her the location of the real Director. When the player frees the real Director, he will give the player the Card Key, which opens the door on 3F of the Radio Tower and leads to the Rocket Executive currently in charge of the group. The player defeats the executive and Team Rocket officially disbands for a second time. The Director rewards the player with a Clear Bell.

Throughout the adventure, the player will also come across, a Legendary Pokémon that traverses Johto after the player awakens the three Legendary beasts from their sleep at the Burned Tower. Unlike and, Suicune takes notice of the player; similarly, Eusine shows interest in Suicune, having sought it for ten years and finally catching a glimpse of it thanks to the player. As Eusine challenges the player to a battle near Cianwood City, it becomes clear that Eusine wants to earn Suicune's respect so that he can find out what it is that it looks after. However, it is when the player is entrusted with the Clear Bell that the allow them to enter the Tin Tower, where Suicune has arrived to put them to the test. Later in the story, after the player has proven their ability to touch the souls of Pokémon by catching all three of the Legendary beasts, returns to the Tin Tower after 150 years of testing humans from afar.

As in all previous games, the main goal of the player is to defeat all the Gym Leaders of Johto, win all eight Badges, and take on the and the current Pokémon League Champion. Afterward, the player will be able to travel to the region of Kanto and take on the Kanto Gym Leaders for their Badges. After winning all eight Badges, Professor Oak will give the player permission to go to Mt. Silver and face the protagonist from Generation I,.