His association with Francis Drake, on a 1577 voyage to raid Spanish treasure fleets, ended in a shipboard trial for treason and witchcraft, and Doughty's execution.
Although some scholars doubt the validity of the charges of treason, and question Drake's authority to try and execute Doughty, the incident set an important precedent: according to a history of the English Navy, titled To Rule the Waves: How the British Navy Shaped the Modern World by Arthur L. Herman, Doughty's execution established the idea that a ship's captain was its absolute ruler, regardless of the rank or social class of its passengers.
[citation needed] Drake, Doughty and John Wynter left Plymouth, England in 1577, purportedly on a simple trip to Alexandria.
[4] The fleet arrived at Puerto San Julián, a natural harbour in Patagonia in the Santa Cruz Province of Argentina on 20 June.
The main body of evidence against Doughty is referenced in manuscripts found in the British Library and compiled in William Sandys Wright Vaux's edition of The World Encompassed, based on a log kept by Drake's chaplain, Francis Fletcher.
The statements could be interpreted as seditious, but would not be likely to be judged mutinous by a court of law (examined at length in Robinson and Hannay; the charges are reproduced in Vaux).
Kelsey concludes that Drake wanted to set a stern example against indiscipline in the crew; his choice to hold Doughty's trial on the same spot where Ferdinand Magellan had executed his mutineers could hardly have been coincidental.
In January 1580, when Drake became stranded upon a reef off the Celebes Sea, the ship's chaplain Francis Fletcher gave a sermon connecting their woes to the unjust demise of Doughty.
For this action, Drake not only relieved Fletcher of his duties but chained him to a hatch cover and, despite his obvious lack of authority to do so, pronounced him excommunicated.
[8] There was also gossip about the inexplicable promotion of the carpenter, Edward Bright, to the position of master of the ship Marigold, which was inevitably read as payment for falsifying testimony against Doughty.