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The storyline of Pokémon HeartGold and SoulSilver closely mirrors that of Gold and Silver, with additional elements from Pokémon Crystal. The protagonist , Ethan or Lyra , starts their quest in New Bark Town, tasked by Professor Elm to visit Mr. Pokémon. Elm provides one of three Pokémon—Chikorita, Cyndaquil, or Totodile—for the task. After the player discovers that Mr. Pokémon's excitement is about an Egg, they return to New Bark Town. There, they encounter a red-haired boy who has stolen a Pokémon from Elm's lab—the one weak against the player's choice. After the player defeats him and returns, they report his name (which defaults to Soul in HeartGold and Heart in SoulSilver if not chosen by the player) to a police officer investigating the theft. Elm, fascinated by the Egg, asks the player to keep their Pokémon and encourages them to challenge Johto's eight Gym Leaders and the Pokémon League. The player then sets off towards Violet City for their first Gym battle.
Upon reaching Violet City, players are required to defeat Elder Li in Sprout Tower before challenging the Violet City Gym. After Li's defeat by Silver, the player's victory over Li rewards them with Flash . Following Falkner's defeat and the acquisition of the Zephyr Badge, Elm's assistant presents the player with an Egg, which eventually hatches into Togepi. Traveling south to Azalea Town via Route 32 and Union Cave, the player encounters the reformed Team Rocket, notorious for their previous disbandment in Kanto. They are harvesting Slowpoke tails, considered sacred in Azalea, for profit. Kurt, a local Poké Ball craftsman, outraged by this, enlists the player's aid to expel Team Rocket and rescue the Slowpoke. Despite injuring himself in Slowpoke Well, Kurt urges the player to battle the organization with their Pokémon. Once Team Rocket is expelled from Azalea, Kurt rewards the player with a Lure Ball and offers to craft specialty Poké Balls from any Apricorn, daily. After conquering Bugsy for the Hive Badge and besting Silver again, the player ventures into Ilex Forest to retrieve the Charcoal maker's Farfetch'd and obtain HM01Cut , enabling navigation through Ilex Forest to Route 34 . There, a Pokémon Day Care capable of nurturing two Pokémon simultaneously operates, consistent with other Generation IV games.
In Goldenrod City, players aim for their third badge, the Plain Badge. Defeating Whitney earns them this badge and a SquirtBottle, which is used to clear the odd tree on Route 36 . On Tuesdays, Thursdays, or Saturdays, they can participate in the Bug-Catching Contest at National Park on Route 35 . Meanwhile, in Ecruteak City, Bill, creator of the PC Pokémon Storage System, completes repairs on the Time Capsule. Upon the player's arrival, he invites them to his parents' house in Goldenrod to receive an Eevee. Ecruteak City also houses a Gym where Leader Morty, a Ghost-type specialist, contends for the Fog Badge. The Legendary beasts are encountered in the Burned Tower, scattering across Johto. Additionally, the player meets Eusine, who is researching the Burned Tower with a particular focus on Suicune.
The journey continues as the player traverses Route 38 and Route 39 to reach Olivine City. There, they discover from Silver that Jasmine, the Gym Leader, is currently unavailable because she is tending to the lighthouse's Ampharos, which needs special medicine from Cianwood City. The player then surfs across Route 40 and Route 41 to Cianwood City, where they meet Chuck, the Fighting-type Gym Leader, who awards them the Storm Badge. After obtaining the medicine from the Cianwood Pharmacy, the player returns to Olivine City. Jasmine, now able to treat her Ampharos, resumes accepting Gym challenges, specializing in Steel-type Pokémon. With the sixth badge, the Mineral Badge, in hand, the player sets off for Mahogany Town via Route 42 , only to find the Gym obstructed by a man and the path to Route 44 and the Ice Path blocked by another man selling Rage Candy Bars.
The player travels north to Route 43 and the Lake of Rage. At the gate, two Team Rocket Grunts demand 
1000 for passage. At the lake, the player encounters the Red Gyarados. Defeating, capturing, or fleeing from it yields the Red Scale. Lance, a caped man, meets the player on the shore and discloses Team Rocket's secret hideout. The player and Lance head to Mahogany to infiltrate the hideout. Team Rocket's scheme involved emitting sound waves to force Magikarp in the lake to evolve into Gyarados, resulting in the Red Gyarados phenomenon. After the player overcomes the Team Rocket members and halts the sound wave machine, they are eligible to challenge Pryce, the town's Ice-type Gym Leader.
After defeating the Gym Leader and securing the Glacier Badge, the player is alerted by Prof. Elm to a peculiar radio broadcast by Team Rocket, seeking their absent leader, Giovanni. The player heads to the Goldenrod Radio Tower for investigation. There, a Team Rocket Grunt bars entry, stating it's restricted to members only. In the tunnel, another grunt, under the guise of recruiting, outfits the player in Team Rocket attire, granting them access to the tower. However, Silver appears, chastising the player for their disguise. It becomes clear that Team Rocket has seized control of the tower. Reaching the top floor, the player encounters the Radio Tower director, only to realize he's a Team Rocket impersonator, and the real director is confined in the basem*nt of Goldenrod. In the basem*nt, Silver confronts the player again, determined to single-handedly take down Team Rocket, while still grappling with his treatment of his Pokémon. Deeper in the basem*nt, the player locates the genuine director, who hands over the Card Key, enabling access to the upper levels of the Radio Tower.
After defeating all Team Rocket members and their executive s, leading to their disbandment, the player is rewarded with either a Rainbow Wing to meet Ho-Oh in HeartGold or a Silver Wing for Lugia in SoulSilver. The journey continues through the Ice Path to Blackthorn City, where Clair, the Dragon-type Gym Leader, awaits. Clair requires the player to pass a test in the Dragon's Den to earn the Rising Badge. Once all 8 Badges are collected, Professor Elm presents the player with a Master Ball and suggests meeting the Kimono Girls. Victory over the Kimono Girls allows the player to encounter Ho-Oh at the Bell Tower in HeartGold or Lugia at the Whirl Islands in SoulSilver, before proceeding to Kanto, east of New Bark Town.
Starting from New Bark Town, the journey to the Pokémon League heads eastward, traversing Route 27 to enter Kanto, then proceeding along Route 26 and through Victory Road, leading up to the Indigo Plateau. Upon reaching the end of Victory Road, the player is once again challenged by Silver for a battle.
The Elite Four challenge awaits players who have collected all eight Badges. Upon entering the League, they must confront each member in succession. The first is Will, a trainer of Psychic-type Pokémon, followed by Koga, a master of Poison-types. Next is Bruno, who favors Fighting-type Pokémon, and then Karen, who is known for her Dark-type Pokémon. Defeating these four leads to a final showdown with the reigning Champion, Lance, previously encountered at the Lake of Rage. Following Lance's defeat, Professor Oak and DJ Mary from Pokémon Talk arrive to offer congratulations. Lance escorts the player to a private room, declaring their induction into the Hall of Fame, as the credits begin to play.
Post-game
The player returns to their bedroom in New Bark Town, heads downstairs, and receives a message that Professor Elm has something for them. At his lab, the player is given an S.S. Ticket for the fast ship S.S. Aqua, which is bound for the region of Kanto, home to many rare Pokémon. Upon boarding the ship in Olivine City, the player is approached by a Gentleman searching for his granddaughter who has wandered off. After scouring the ship, the player encounters a sailor upset about his sleeping co-worker. The player wakes him with a battle, and he hurries off to his duties. Eventually, the player discovers the missing girl at the ship's lower level. She invites the player to a game of hide and seek, and after being found twice, she agrees to return to her grandfather. The grateful man thanks the player as the ship docks in Vermilion City, Kanto.
Eager to challenge the Kanto Gyms, the player defeats Lt. Surge in Vermilion City, an Electric-type specialist, and claims the Thunder Badge. Heading north to Saffron City, the player bests Sabrina, the Psychic-type Gym Leader who had foreseen their arrival three years earlier, and secures the Marsh Badge. In Saffron, the player meets the Copycat , who has lost her Pokémon doll. The player retrieves the Lost Item from Vermilion's Pokémon Fan Club and returns it to the Copycat, who rewards them with a Pass for the Saffron Magnet Train.
The player heads west from Saffron to Celadon City, challenges Erika in the Gym, and earns the Rainbow Badge. Returning to Saffron and then eastward, they reach the Kanto Power Plant, only to discover a crucial machine component has been stolen, halting operations. Heading north to Cerulean City, the player learns of a suspicious figure lurking near the Gym. Further north on Route 24 , they encounter and defeat a Team Rocket grunt attempting to resurrect the team, unaware that the player had previously disbanded it in Johto. The defeated grunt reveals he dropped the part in the Cerulean Gym. After challenging the Nugget Crew and encountering Misty at Cerulean Cape, the player battles her in the Cerulean Gym, wins the Cascade Badge, and recovers the Machine Part. With the part returned, the Power Plant resumes function.
Next, the player traverses Rock Tunnel to Lavender Town, finding the old Pokémon Tower transformed into a Radio Tower. The director gifts them the Radio Expansion Card for restoring power to the Power Plant. The journey continues across Silence Bridge and through Routes 13 , 14 , and 15 , culminating in a battle against Fuchsia City's Gym Leader Janine, a Poison-type specialist, where the player secures the Soul Badge.
Upon returning to Vermilion City, the player remembers the large Pokémon slumbering at the entrance of Diglett's Cave on the town's eastern border. Activating the Poké Flute Station on their radio rouses and irritates the Pokémon, a colossal Snorlax. Whether they capture, defeat, or flee from it, the player proceeds through Diglett's Cave and emerges on Route 2 , just below Pewter City. Heading north to Pewter City, the player confronts Brock and his Rock-type Pokémon, securing the Boulder Badge.
The journey continues southward across Route 2 and through Viridian Forest, leading to Viridian City. The player then heads further south to Pallet Town and takes to the waves towards Cinnabar Island. There, they encounter Blue , who recounts the destruction of the town that once stood on the island due to a volcanic eruption, necessitating the relocation of the town's Gym Leader to the Seafoam Islands. After Blue returns to his Gym in Viridian, the player ventures east to the Seafoam Islands, challenges Blaine in his Fire-type Gym nestled within the islands, and strives to win the Volcano Badge.
The player returns to Viridian City to challenge Blue in his Gym, which has no type specialty, and wins the Earth Badge. Then, the player revisits Pallet Town to see Professor Oak in his lab. Oak, recognizing the player's collection of all Kanto Gym Badges, hands over HM08 and grants access to Mt. Silver, a perilous mountain off-limits to average Trainers. There, the player seeks out Red , the reigning Kanto champion for three years, who is in constant training. At the mountain's peak, the player finds Red, silently training, and initiates a battle. Following an intense fight, the player emerges victorious over Red, claiming the title of Kanto's new champion. Red departs wordlessly as the credits begin to roll once more.
