The Pirate Master is the main antagonist of Genies in Sequin Land to seal him away from the world in a lonely grave on an isolated island. Risky Boots used to be his first mate until his defeat, after which she inherited his Tinkerbats and Pirate Gear. As an added insult to injury, Risky also took his face and turned it into her bustier and belt.. A frighteningly powerful creature, it took the combined power of all the
Sensing that the power of light magic has vanished from Sequin Land, the Pirate Master begins to stir and unleashes a curse on the surrounding islands, transforming most of the Tinkerbats into vicious Cacklebats and gathering dark energy from the evil-infested dens of monsters.
Forced to work together, Risky and Shantae manage to seal up the dens and cut off the flow of dark magic, but they are unable to stop the Pirate Master's revival and Risky is captured by her vengeful ex-master.
Shantae chases The Pirate Master to the roof of Sequin Land Palace, she tries to fight the Pirate Master and initially wins. Should the player manage to defeat all the cackle bats in their first playthrough, The Pirate Master will take back his Pirate Gear from Shantae and becomes even more powerful. He eventually demands that Shantae give him the dark magic she had taken from his Cacklebats in exchange for Risky's life. Shantae accepts and releases the collected magic, which has turned to light magic. Reabsorbing the magic into herself, Shantae regains her genie powers and is able to critically weaken the Pirate Master, allowing Risky to use Ammo Baron's long-range cannon to destroy him once and for all.
Shantae fails to defeat the Pirate Master and the latter escapes. Risky vows to go after her former master, to Shantae's disapproval over her concerns of Risky's curse. Risky ignores her and says that the curse will eventually overtake her anyways and sets off. Shantae is upset over not being able to break the curse.
Though powerful, the Pirate Master sticks to a very rigid attack pattern.
- The Pirate Master will teleport around the area, appearing on either side or the middle of the screen. Hair-whip him at each interval. After four teleports, his next two will be followed with a wide-reaching blast of dark magic. Getting hit by these blasts really hurts (two full Hearts a hit!). Either get some distance and crouch or use a Bubble Shield.
- He will then summon skeletal platforms to sway back and forth while he warps between them and fires more dark magic towards the ground. It's best to concentrate on dodging at this point.
- When he comes back to the ground, crosshairs appear to telegraph where deadly laser beams are going to fire. The lines in them will show which way the beams will fire. If no beams are firing near the Pirate Master, Shantae can get close and tear him up with hair-whips and Super Pike Balls. Otherwise, find a safe spot and use the hat and cannon if needed. After this, the Pirate Master repeats from the first step.
- The Pirate Master has 1000 HP so go all out with your items if you need to.
If Shantae did not kill all 20 Cacklebats and collect their Dark Magic, the battle and the game will end after Phase 1 and a downbeat ending will play. Otherwise, the battle will continue.
The Pirate Master has taken the Pirate Gear away from Shantae, limiting her to hair-whips and items for attacks, and he has now grown into a giant. Only his head is vulnerable to attack. Like before, he has 1000 HP.
- He starts by firing three cannonballs, which bounce across the screen. Stand near the middle of the screen where the first one will hit, then run forward to dodge the rest. They will make two passes. Shantae can get some hits in while he's firing.
- Next, he brings down swords from the sky. There is only one spot where the swords won't hit, so run there. Getting hit results in losing two and a half hearts (10 HP) but it's easy to reach the safe gap in the attack.
- The Pirate Master summons pistols next. Four pistols will spin in the center of the screen and fire dark magic in expanding circles. Simply stay put and calmly wait for an opening to dodge each incoming shot. Using Bubble Shields will also help.
- Finally, platforms appear and shadows of the Pirate Master's first form will stand on them to shoot dark magic. Climb the platforms and whip away the shadows, then hit the Pirate Master's head with everything available. Super Pike Balls and Super Monster Milks should not be spared at this point. Eventually, he will start over with the cannonballs.
Shantae has regained her genie powers. Her hair-whip now hits for 999 damage, but the Pirate Master has gotten a power boost as well. Now he has over 100,000 HP! This means that he takes 101 hits to defeat without the use of items. Note that Monster Milk and Super Monster Milk do not boost Shantae's hair attack damage any further.
- The Pirate Master will use the same four attacks as before and in the same order, but now he throws added tricks into them. He will now fire four cannonballs. Use the same method of dodging as before but before the fourth cannonball, quickly change directions to dodge it. He then move the swords around to make the safe-spot harder to reach. Just keep moving with the safe spot and you should still have enough reaction time to find the safe spot. He will then throw the pistols at Shantae once they have all fired. To avoid the pistols, go all the way to either side of the screen and crouch. They should fly overhead and go off-screen.
- Once enough damage has been inflicted, Risky will provide support from Scuttle Town by commandeering a cannon. As Shantae continues to fight, crosshairs must be maneuvered into position to hit the Pirate Master's head with cannon shells. The shells take time to reach the palace once fired, so Shantae must keep hair-whipping him so that he stays put long enough for the shell to hit. The only real piece of advice here is to have a good mashing finger on the attack button and a separate finger on the gun fire button, as that button controls the cannon now. With each hit, he'll move faster and spit dark magic to impede Shantae's targeting. Four direct hits will finally end this long and arduous battle.