The game's story focuses on a young "half-genie" by the name of Shantae. Having been appointed as the Guardian Genie of a small fishing town, Shantae's life is fairly quiet. That quickly changes when a gang of pirates, led by the sinister Risky Boots, attacks the town and steals a prototype steam engine from the town's resident Relic Hunter, Mimic.

Shantae soon finds herself traveling far and wide across Sequin Land, determined to retrieve the steam engine and foil Risky's wicked plan.

• Shantae – The heroine, a young half-genie charged with protecting the fishing port of Scuttle Town. Young and somewhat naïve, Shantae's strong sense of justice nonetheless propels her into action. Her main form of offense is using her magically endowed ponytail as a crude whip. In addition, she is capable of transforming into various creatures (a monkey, an elephant, a spider and a harpy) via the use of magical dances. Having failed to protect Scuttle Town from Risky Boots, Shantae finds herself obligated to find Risky and get the stolen steam engine back.

• Risky Boots – The nefarious lady-pirate Risky Boots, and Shantae's nemesis, is known throughout Sequin Land for her love of wealth, power, and all shiny things. Risky is an unchallenged and self-appointed 'queen of the Seven Seas', and will caution and toll anyone to think otherwise. Risky is a villain with the skills and luck usually reserved for the good guys. Capable, dominating, and deadly, Risky isn't afraid to claim what's not hers. She commands an endless army of Tinkerbats who follow her orders without question, building her weapons of war and scavenging the resources that make her schemes become reality.

• Tinker Bats – Tinkerbats are Risky's silent shadow army. Individually they are not very formidable in battle, and therefore tend to huddle in groups of 3 or more. They are intelligent and skillful, yet skittish and non-communicative. Their loyalty knows no bounds, and like drones serving a queen they act as an extension of Risky's will. Where Risky harvests her Tinkerbats is unknown.

• Mimic – Old Uncle Mimic is one of the Relic Hunters... a consortium of explorers that attempt to advance the future by excavating secrets of the past. Mimic is the closest thing Shantae has to a family. He lives in his workshop in Scuttle Town, where he houses hundreds of ancient objects. Since townsfolk tend to be skeptical and stand-offish to Relic Hunters (and genies), he and Shantae make a great pair. Shantae makes Mimic her project, and refuses to let him grow old, sloppy, or comfortable. Although she can get on his nerves at times, Mimic genuinely loves Shantae and strives to keep her safe. Although Shantae has no idea, Mimic is a retired hero of days long gone and still contains dormant skills that could awaken if provoked.

• Bolo – Shantae's sparring partner is a slow-witted knucklehead with a serious lack of reasoning skills. He's hardly awake until he springs into action...usually at the chance to be a hero. As a fighter, Bolo is very efficient and skillful, as though these moments of competence are sustained by his regular state of mental hibernation. Bolo has eyes for Risky Boots and nearly anything else remotely female, although a brotherly comfort level keeps Shantae outside his level of vision. Bolo is commonly used as a punching bag or stool pigeon by Rotty, Sky and Shantae. Mimic often uses Bolo as an errand boy, which given his single track mind works fairly well.

• Sky – Shantae's lifelong friend and ally, Sky is a war bird trainer whose profitable egg hunts often span the known reaches of Sequin Land. Sky can't wait for Shantae to see more of the world and life's surprises, and seems to be in a hurry to grow up. Sky is a sort of desert rat, always nesting in out of the way places at length. For this reason, Shanatae and Sky have tend to have more unexpected reunions than they do planned visits. Even apart, their friendship is a strong one, and Sky's opinions hold equal value to Uncle Mimic's in Shantae's mind. Sky keeps a war bird named Wrench, and she is rarely seen without him. Wrench is a dangerous weapon, and is totally reliable, even following Shantae's orders. For some reason, Wrench regards Bolo as prey, and takes every opportunity to prove it.

• Rottytops – Rotty is a free sprit... friendly, energetic, and headstrong. However, she is also extremely untrustworthy, crafty, and manipulative. She loves ruffling peoples feathers or guiding then down the wrong path. She's a tease and a shameless flirt on a near-criminal level, and her scruples know no boundaries. As a family member in a Zombie Clan, Rotty travels the land by caravan gaining worldly skills and threatening to eat peoples brains. She has 2 nasty brothers that seem capable of bringing out the worst in her whenever they're all together. Rotty is obsessed with Shantae, and the challenge of corrupting her pure nature.

Shantae was generally well received by critics. IGN gave the game a 9 out of 10, calling it a "wonderful platform adventure".GameSpot scored it a 7.7 out of 10, claiming it to be a "fine example" of a portable platformer.GamesRadar listed Shantae as one of the titles they want in the 3DS Virtual Console.

A Shantae sequel was planned for the Game Boy Advance, and proposed screens resemble a port with updated graphics. It is assumed to have been canceled. As with the original game, Shantae Advance was developed by Matt Bozon on his own time.

On September 15, 2009, a sequel titled Shantae: Risky's Revenge was revealed as a downloadable DSiWare title on Nintendo of America's 2009 Holiday lineup, with a tentative 2009 Q4 release date. Details on the 3-part episodic sequels were revealed in the November 2009 issue of Nintendo Power. However, plans for the episodic release were cancelled, and the game was instead released as a standalone DSiWare title on October 4, 2010. The game was later ported to iOS. A third game, Shantae and the Pirate's Curse, has been announced for release on the Nintendo 3DS eShop.

Shantae is currently planned for digital re-release via the Nintendo 3DS Virtual Console.