The story begins with the player riding in a moving van with Professor Baro (who replaces Professor Birch's role in Pokémon Ruby, Sapphire, and Emerald Versions). The player and his mother have just moved in to Breeze Town of the Corna region, which is a heavily modified Hoenn region. Coincidentially, the player's rival and his/her mother have moved in to the next-door house around the same time. Upon meeting the rival, he/she immediately develops a crush on the player while doing a poor job at hiding it.
The player later encounters Professor Baro at "BREEZE WY," where he is being chased by a wild Sever (Poochyena clone). Professor Baro asks the player to take a Poké Ball out of his bag, where the player may choose his/her starter Pokémon. After choosing, the player battles and defeats the Sever. After rescuing Baro, he lets the player keep the chosen Pokémon as thanks for saving him. He asks the player to meet up with his/her rival at "ROCK CN." After the player battles and defeats the rival at "ROCK CN," they return to Baro's lab, where they each receive a Pokédex and some Poké Balls. From there, the player may travel to more cities and towns, battle and defeat the Gym Leaders of the Corna region, and challenge the Pokémon League. Along the way, he/she will encounter Band Ambar, an electric-based evil organization led by Amber whose goal is to "inflate the sun" to make Electric-type Pokémon more powerful.
Though Pokémon Quartz is a hacked version of Pokémon Ruby, the Pokémon Gyms have been modified to have different typings from the original set. There are eight Pokémon Gyms in Corna, each with their own type affiliation. The Gym Leaders are Betti (Bug), Fausto (Ghost), Max (Ground).
The PokéBar is the same exact feature as the PokéNav in Pokémon Ruby, Sapphire, and Emerald Versions. It has the ability to check the Condition of the player's Pokémon; has the feature Trainer's Eyes, which keeps data on various Trainers and alerts the player when the Trainers want rematches; and can displkay the Ribbons that Pokémon has earned. Due to the lack of a world map, viewing the map will cause the game to enter a black screen in which the player will be unable to exit out of until he/she resets the game.
Despite the game's artwork being represented by a Gyarados on a red background, the game itself has none of the official Pokémon copyrighted by Nintendo. Instead, all Pokémon sprites, their typings, and sometimes their moves have been modified with the exception of their battle cries. The designs of the "Fakemon" have been criticized for their bizarre appearances and sometimes misleading typings (the most notorious example being Babos).
Due to being a ROM hack, Pokémon Quartz has numerous glitches. Particularly, the Game Boy Advance cartridges contain the most errors while the ROM patch works very well with the emulation program VisualBoyAdvance.
- Due to the lack of a world map, viewing the map (whether through a poster, the Pokédex, or the PokéBar) will cause the game to enter a black screen in which the player will be unable to exit out of until he/she resets the game.
- Berries grow at a much faster rate, making it more likely for the trees to "die" out when left unattended for a certain amount of time.
- Pokémon Marble Version is the sequel to Pokémon Quartz Version, being a Pokémon FireRed ROM hack. It is currently available as a beta release.
- Professor Baro and Baro-chan are self-insert characters of the ROM hack's creator.
- In Deathland, there is a ninja NPC known as Garo. The name and the NPC's dialogue is an allusion to an enemy in The Legend of Zelda: Majora's Mask.