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Trinidad was the flagship of Ferdinand Magellan, which he personally captained during his voyage across the Pacific Ocean. It was staffed with a number of crewmembers, including Juan Sebastian Del Cano as its first mate. While out at sea, the ship was plagued with problems, including a mutiny against Ferdinand, a scourge of scurvy, a lack of food, and, in 1521, Ferdinand's Astrolabe is stolen by a time traveling Bowser (according to Mario's Time Machine). Mario later travels to the Trinidad himself with the astrolabe in hand and, not knowing exactly what is going on nor who the astrolabe belongs to, questions the ship's crew about current events. Eventually, they tell him that the Astrolabe belongs to Ferdinand, and Mario returns it to him before time traveling back to the present.
In the NES release, Bill Blasters make a cameo aboard the ship, although they do not fire.