During the annual Relics Hunters Expo, Shantae and her friends watch her Uncle Mimic unveil his latest find: an ordinary-looking lamp encased in stone. As they wonder its purpose, Risky Boots and her pirates crash the expo and steal the lamp. Shantae battles her, but is knocked out, allowing Risky to escape. Blaming the half-genie for the town being in disarray and failing to do her job properly, Mayor Scuttlebutt fires her as Scuttle Town's Guardian.

Despite no longer being a Guardian Genie, Shantae still decides to take responsibility to stop Risky Boots' newest plot. Mimic reveals to Shantae that three hidden magic seals are necessary to release the lamp's magic, and Shantae sets out to find them. With help from her friend, the zombie Rottytops, she learns that the seals are in possession of three treasure hunters, the Barons of Sequin Land, whom she will have to confront to obtain the seals. While she pursues the Barons, Risky tricks Rottytops and her brothers into kidnapping Mimic for her, promising them a lifetime supply of coffee needed to maintain their sanity, and particularly, Shantae's brains for Rottytops. Shantae, now in possession of the three seals, reaches them as Risky reveals her deception. Shantae surrenders the seals in exchange for Mimic's life. Risky then sucks Shantae's magical half into the lamp before revealing to Shantae that it has the power to capture and enslave genies, then she unleashes the magical half as the evil Nega-Shantae, ordering it to destroy Shantae. Shantae manages to defeat her counterpart, and flees from Risky's hideout as it collapses. She reunites with her friends, who promise to help her defend Scuttle Town and adjust to her new life as a human. The Mayor, impressed by her commitment, re-hires her as the town's Guardian.