Much like Pokémon FireRed and LeafGreen revisited the Generation I story of Kanto, HeartGold and SoulSilver retell the story of Johto, with the player’s starting area being New Bark Town. While the games feature several expansions in key areas, the overall plot follows the same direction as the original Gold and Silver. Some aspects exclusive to Crystal are also included. Like FireRed and LeafGreen could link up with Ruby, Sapphire, and Emerald to complete the Pokédex by trading regionally exclusive Pokémon, HeartGold and SoulSilver can link up with Diamond, Pearl, and Platinum to obtain Pokémon unavailable in Johto and Kanto, such as the Sinnoh starters.

Kris, despite being the female counterpart of Crystal’s player character Ethan, is not included as the female player character, with a new character instead taking her place. Whether she is chosen to be the player character or not, this new character will still appear in the game, taking a pseudo-rival role similar to the unselected characters of Ruby, Sapphire, Emerald, Diamond, Pearl, and Platinum.