After Risky Boots clears the "Risky's Hideout" platforming segment she'll order her Tinkerbats to activate the Dynamo to which the stage is raised towards it. Before Risky Boots attempts to activate the machine Shantae interrupts her. She explains how her friends were able to revert the magical inversion process before doing battle with Risky Boots.
As a boss, Shantae runs and jumps around the room, attacking using forms from her campaign. As usual, each transformation requires Shantae to perform a short dance, during which she is vulnerable to attack. Unlike most bosses, Shantae's visual appearance will change after receiving a significant amount of damage, which also signals a small increase in her general speed.
- Monkey - Shantae will use Monkey Bullet to dash around the stage at random, occasionally launching herself at Risky.
- Elephant - Shantae will launch upwards and smash down as a giant elephant. Her impact zone is marked by clouds of smoke; Risky should move away from the smoke to avoid being squashed, allowing her to land a few hits before Shantae returns to her normal form.
- Mermaid - Shantae will jump into the air and spin rapidly, firing waves of bubbles at Risky.
- Crab - Two waterfalls will appear on the sides of the room as Shantae jumps off of the stage. She begins moving up and down one of the waterfalls, occasionally dashing across the screen to enter the other waterfall. Shantae's location can be observed by bubbles emerging from the waterfall, allowing Risky to dodge as appropriate.
- Harpy - Shantae will fly off the top of the stage to attack Risky by swooping down in an arc from left to right.
- Spider - Shantae will move off the top of the screen and rain spider venom onto the stage. After dodging the venom, Risky should keep moving to avoid being hit when Shantae drops back down.
- Bat - Shantae will darken the entire stage, save for a small circle of light around her bat form. She will then fly around the stage, emitting a screech sound effect if Risky has entered the light radius; the pirate captain should take care not to get hit by the half-genie's flight.
- Mouse - Shantae quickly runs around the stage, periodically reverting to her human form in an attempt to damage Risky. She has to pause briefly before transforming, giving Risky time to move away; alternately, she can hover out of Shantae's attack range with liberal use of her Cannon Jump.
Upon destroying Shantae, Risky attempts to activate the Dynamo, only for it to malfunction. To her surprise and annoyance, the Tinkerbats did not correctly construct the machine; as a result, it explodes with enough force to destroy her Hideout and send her flying away. Having failed to capture Sequin Land, Risky berates her Tinkerbats once more before the game cuts to credits.
- As Pirate Queen's Quest is heavily implied to be Risky's biased account of Half-Genie Hero's events, her final battle with Shantae (or, at least, the outcome) is non-canon.
- Shantae's boss fight draws direct inspiration from Nega-Shantae's boss battle in Risky's Revenge. She uses all of Nega-Shantae's attacks in addition to several new moves; the most notable change is the horizontal dash used by Nega-Shantae's Monkey form was given to Shantae's Crab form.
- The only transformations Shantae doesn't use in her boss battle are the Dryad, Tinkerbat (backer-exclusive), Gem Pot, and Blobfish. Interestingly, all of these dances come from Tuki.
- Shantae is the only boss in the game whose idle sprite changes after receiving significant damage.