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The Captain of the Piratians appears in the Oracle games. He is revealed to be Queen Ambi's long-lost love, transformed into a Stalfos, making him one of the many Stalfos to become transformed yet retain their original personalities. Throughout the game he searches for the Pirate's Bell. He remains unnamed, except for his title of Captain.
Oracle of Ages
In Oracle of Ages, the Captain appears trapped in a large ring of whirlpools, accessible after the seventh dungeon. Once Link gives the Captain the Zora Scale he obtained recently, the Captain is able to escape, declaring he and his crew are off to Holodrum, but first giving Link the Tokay Eyeball.
Oracle of Seasons
In Oracle of Seasons, the Captain's ship has become trapped in the desert, and the crew is in Subrosia, while the Captain searches for his bell. Once Link finds and fixes the bell, the crew manages to free the ship and sets sail once more, only to be overcome with seasickness, stopping on the beach west of Horon Village.
In the Legend of Zelda Manga
In the Legend of Zelda manga, the Captain is the individual who tells Link and Ralph of Veran's weakness. While he was alive, he served as a knight under Queen Ambi, and later became her lover. Soon after meeting Link he set sail for Labrynna, but was caught in a storm.
Theory
It is theorized by many fans that Captain Stalfos from Freshly-Picked Tingle's Rosy Rupeeland is the same captain, or related in some way as they both command a similar crew of Stalfos pirates.