The game tells the story of Geralt of Rivia, a Witcher – a genetically enhanced human with special powers trained to slay monsters. The Witcher contains three different paths, which affect the game’s storyline. These paths are: alliance with the Scoia'tael, a guerrilla freedom-fighting group of Elves and other non-humans; alliance with the Order of the Flaming Rose, whose knights protect the country of Temeria; or alliance with neither group to maintain "Witcher neutrality".

In the game’s opening cutscene, Geralt is tasked with curing King Foltest's daughter, Princess Adda, of a curse that transforms her into a feral monster. Years later, a group of Witchers find an amnesiac Geralt unconscious in a field and take him to the Witcher stronghold of Kaer Morhen. As he struggles to recall his memories, the castle is attacked by a gang of bandits named the Salamandra. The Witchers and sorceress Triss Merigold battle the invaders, but the mage Azar Javed and the assassin Professor escape with the mutagenic potions that genetically alter the Witchers. The Witchers head off in different directions to find information on the Salamandra.