Pokémon Gold and Silver Versions/Plot/Main Game

begins their journey from New Bark Town, running an errand for Professor Elm to Mr. Pokémon's house to discover what he was so excited about. Elm supplies the player with one of three Pokémon,, , or , for this errand. After Mr. Pokémon's discovery turns out to be an, the player returns to New Bark, only to find that a suspicious seen lurking outside of Elm's lab earlier has stolen one of Elm's Pokémon— the one that the player's choice is weak to, coincidentally. Upon defeating him and returning to New Bark, the player gives the name of the boy (the player can choose any name, provided it fits under the seven-character limit; his name defaults to Silver or Gold) to a police officer who has come to investigate the incident. Elm is amazed by the Egg and insists on studying it, allowing the player to keep the Pokémon they traveled with as a starter Pokémon. From here, he encourages the player to journey across Johto and challenge the eight Gym Leaders, Falkner, Bugsy, Whitney, Morty, Chuck, Jasmine, Pryce, and Clair, and eventually the Pokémon League (though this is a long way off). With the first Gym in nearby Violet City, the player heads off on their adventure.

After defeating Falkner for the, Elm's assistant appears to give the player the Egg, which will later hatch into a. Heading south towards Azalea Town by way of and Union Cave, the player meets up with the villainous Team Rocket, formed again after it was disbanded three years prior in the neighboring Kanto region by. They are cutting off the tails of the that are legendary in Azalea, intending to sell them for a large profit. Kurt, a local maker of specialty Poké Balls, is greatly angered by this, and requests the player's help in chasing away Team Rocket and saving the Slowpoke. Though he falls into Slowpoke Well, hurting himself in the process, he begs the player to continue on to fight the organization with their Pokémon. After this has been done, and Team Rocket is chased away from Azalea, Kurt gives the player a and will make his specialty Poké Balls when brought any kind of Apricorn, one per day. After defeating Bugsy in the Azalea Gym for the and defeating the red-haired boy (Silver) once again, the player can journey into Ilex Forest to find the Charcoal maker's  and get. With this, Ilex Forest can be navigated through towards. On Route 34, a Pokémon Day Care is set up, however, unlike the one found in Kanto on, it is capable of raising two Pokémon at once. If these Pokémon are similar enough, and if a male and female have been put in together, a Pokémon Egg can be produced.

Venturing into Goldenrod City, the player's third Badge, the, awaits. After defeating Whitney and getting the Badge, receiving a SquirtBottle allows the player to move the blocking  to the north. If it is Tuesday, Thursday, or Saturday, the Bug-Catching Contest will be occurring at the National Park on, as well. In Ecruteak City, Bill, the developer of the PC Pokémon Storage System is performing repairs on the Time Capsule, and as the player arrives, he will finish, asking for them to come visit him in his parents' house in Goldenrod, where he will give away an. Another Gym is in Ecruteak, where the Leader Morty battles for the.

The player goes on through and  to arrive in Olivine City. Once there, they learn from Silver that Jasmine, the Gym Leader, is not available at the moment, since she is taking care of the lighthouse's Ampharos and refuses to leave until the Pokémon is given a special medicine from Cianwood City. The player thus surfs their way through and  to get to Cianwood. There, they encounter the Leader Chuck, who presents the player with the. They get the SecretPotion from the Cianwood Pharmacy and goes back to Olivine. Jasmine, relieved after getting her Ampharos's medicine, goes back to taking Gym challenges. Her Pokémon specialty is of the Steel type. When the player gets their sixth Badge, the, they travel to Mahogany Town, through. The Gym is blocked by a man and the way to and the Ice Path is blocked by another man trying to sell RageCandyBars.

The player heads north to and the Lake of Rage. Upon entering the gate, two s charge them 1000 to go through. When the player gets to the lake, they encounter the Red Gyarados. After the player defeats, catches or flees from it, they receive the Red Scale. A caped man named Lance appears on the shore and reveals Team Rocket's secret hideout to the player. The player goes back to Mahogany and goes through the hideout, along with Lance. Team Rocket's plan was to emit sound waves, inducing the Magikarp in the lake to evolve into Gyarados, which caused the effect of the Red Gyarados. Once the player defeats all the Rockets and disables the wave-emitting machine, they can challenge Pryce, the town's Gym Leader.

Upon defeating the Gym Leader and obtaining the, the player receives a phone call from Prof. Elm about a strange radio signal emitted by Team Rocket, trying to connect with their missing leader, Giovanni. The player goes to the Goldenrod Radio Tower to investigate. Once there, they find the Tower to be taken over by Team Rocket. When the player ascends to the top floor, they find the director of the Radio Tower, only to discover that he has been impersonated by a Rocket and that the real Director is actually locked in Goldenrod's basement. Once the player enters the basement, they are once again encountered by Silver, who intends to defeat Team Rocket all by himself. He still questions the way he treats his Pokémon. Once the player gets to the very bottom of the basement, they find the Tower's real Director. He gives the player the Card Key, so that they can access the higher floors of the Radio Tower.

After clearing all of the Rockets, effectively disbanding them, the player receives either a Rainbow Wing to encounter or a Silver Wing to encounter, in the Gold and Silver versions respectively. The player can either go to the Tin Tower or the Whirl Islands at this point, to challenge Ho-Oh or Lugia, respectively; alternatively, they can go straight to, now unblocked, and through the Ice Path to get to Blackthorn City. There the player can challenge Clair, the Gym Leader. Before giving the player the, however, Clair requires the player go through a test to prove their worthiness. To complete this test, the player must enter the Dragon's Den and retrieve a Dragon Fang. When the player finds the item, they receive the Rising Badge from Clair. Having obtained all 8 Badges, the player returns to New Bark Town, traveling down and.

Professor Elm contacts the player, and awards them with a when visited. From New Bark, the path to the Pokémon League is to the east, across and into Kanto, then across  and through  to Indigo Plateau. When the player reaches the exit of Victory Road, Silver appears again and battles the player.

The Elite Four awaits the player if they have collected all eight Badges. When the player enters the League, they must face all four in sequence. Will, who trains Pokémon, is first, followed by Koga, who specializes in Poison Pokémon. Following is Bruno, who uses Pokémon, and finally, Karen, who specializes in the Dark type. After defeating these four, the reigning Pokémon Champion, Lance, challenges the player to a final battle. After his defeat, and his co-host on Pokémon Talk, DJ Mary, arrive and congratulate the player. Lance then takes the player to a back room and tells the player that they are admitted into the Hall of Fame. The credits roll.