Magellan began methodically exploring the Strait of Magellan upon discovering it on October 21st, 1520. This wasn’t any easy task. The strait is a maze of different channels through a myriad of islands stretching east and west and to the south. To hasten the search, Magellan made a fateful decision. He sent the San Antonio in one direct while he sailed with the armada’s other three ships in a different direction, with the plan being to rejoin in three days.
The San Antonio never appeared at the agreed upon meeting place. Fearing the San Antonio had encountered troubles, Magellan’s ships then spent nearly two weeks searching for the missing ship. The Victoria went all the way back to the Atlantic Ocean in hopes of finding it. Finding no evidence of the ship, Magellan asked pilot and astrologer San Martin to divine its fate. With uncanny perception, and perhaps inside knowledge, San Martin said that the San Antonio’s captain Mesquita was now a prisoner and that the San Antonio was sailing back to Spain.
This was indeed the case. Mesquita, a relative of Magellan, and Pilot Gomez had had a violent argument, with Gomez stabbing Mesquita in the leg and Mesquita returning the favor to Mesquita’s hand. Gomez was one of the most experienced mariners of the armada after Magellan. They weren’t friends. Gomez’s proposal to sail to the Spice Islands had been rejected by King Charles in favor of Magellan’s plan. Furthermore, off Brazil Magellan had essentially demoted Gomez from his position as Pilot Major of the armada. Gomez didn’t harbor warm and fuzzy feelings for Magellan, and given the opportunity he deposed the hapless Mesquita, who earlier, despite warnings, allowed the mutineers to capture his ship in San Julian. And so, Gomez convinced his crew to side with him, and they defected.
The loss of the San Antonio was a serious blow to Magellan’s plans. At 120 tons, it was the largest ship in the armada. The Trinidad was 110 tons while the Victoria and Concepcion were 85 and 90 tons respectively. Thus, the San Antonio carried a disproportionate amount of the armada’s supplies. This loss, and the time lost and food consumed while needlessly searching for the San Antonio, would haunt the armada in the last days of crossing the Pacific Ocean, leading to unnecessary deaths due to starvation and scurvy.