The story takes place around the release of Pokémon HeartGold and SoulSilver. While waiting for SoulSilver, a fan decides to buy a used copy of Pokémon Silver at GameStop. When they start up the game, it initially seems like the cartridge is faulty. It keeps freezing on the Game Freak logo, however eventually it starts up. Instead of starting up as normal, the game defaults to an active file in the Bellsprout Tower.
Gold's name is only given as "...". There are 999 hours of play time on the file, Gold has the max amount of money, and the Pokédex is entirely filled out. When the protagonist looks at the team, it consists of five Unown and one Cyndaquil nicknamed "HURRY". The five Unown spell out "LEAVE". The cartridge seems glitched as it contains oddities like no music, no Pokémon cries, and no trainers in the Bellsprout Tower. The room seems inescapable due to a lack of ladders, however eventually the player finds a way to exit it.
They enter a dark room and use Flash. Upon walking down the hall, they come to a dead end with a sign that says "TURN BACK NOW", with an option to pick yes or no. Their Cyndaquil randomly faints after leaving the room. When they check their team, all six Pokémon have been replaced with new Unown spelling out "HE DIED". The new room is a cemetery with Gold being inside of a hollowed out grave. When they check Gold's profile, Gold's sprite is missing his arms and he looks more stoic.
The player eventually spins downward back into Bellsprout Tower. The difference is that Gold's sprite is completely white. When they check Gold's profile, he's missing his legs and bleeding from his eyes. He also has 32 badges now. The team now featuress five Unown spelling out "Dying" and a level 100 shiny Celebi. The Celebi only knows Perish Song and is missing one eye, one leg, and one arm. After walking through a hall in the tower, the player comes across three generic NPCs which can't be talked to. Eventually, the player comes aross the end of the room. The pillar is chopped in half and there's a transparent Red standing next to it. Without even pressing anything, the player enters a glitched battle with Red.
Each team only has one Pokémon. Gold has his Celebi and Red has a sad looking level 255 Pikachu. After two turns of Perish Song, Celebi uses Pain Split on its own, despite not knowing the move. At the end of the battle, Celebi dies. Pikachu doesn't die alongside Celebi and instead uses Destiny Bond, before proceeding to die. Gold wins the battle. When Red's lose quote comes up, he's missing his head.
Gold appears in his bedroom with a transparent overworld sprite. His profile sprite is now missing everything but his head. Gold now has 40 gym badges and six level twenty shiny Unown that spell out "No more". Gold's sprite doesn't move anymore, giving off the impression that he's floating. Gold's house is empty and he can't interact with the scenery. When he tries to exit the house, Gold just enters a black void. Gold's outline turns white as the player continues south. Finally, he comes across Gold's regular sprite. When spoken to he says "Goodbye forever..." before vanishing. A new text box appears saying that "??? used Nightmare".
Gold returns to the cemetery but without a sprite. When Gold's profile is checked, there's no sprite, he has no badges, and all the Johto gym leader sprites have been replaced with skulls. Gold's team consists of six Unown that spell out "I'm Dead". The game ends with a text box saying "R.I.P. ...".
Pokémon Lost Silver provides examples of:
- Adaptation Expansion: The fan game includes a second storyline, generally known as Lost Silver: Hidden. The creator of the fan game says that this plot was written by the creepypastas original author and given to him for the game.
- Adaptation Name Change: Ethan is referred to as "Gold", likely because his Canon Name wasn't known until HeartGold and SoulSilver's release.
- Dark Fic: It's a story about a creepy cartridge of Pokémon Silver where the player is dead.
- Dead All Along: At the end of the story, the player realizes that Gold has been dead since the very beginning.
- Death of a Child: Gold isn't even thirteen when he died.
- Fan Game: The creepypasta was defictionalized into a game.
- Gender-Neutral Narrator: The reader is never identified by gender.
- Haunted Technology: The cartridge is presumed to be this, though it might be a hack that someone made.
- Maybe Magic, Maybe Mundane: It's unclear if the cartridge is haunted or whether it's a hacked game.
- Riddle for the Ages: Whether the game is of supernatural origin, or a modified version made by a person. And if the the latter, then their reasoning for doing so would also come under this.