He rose to the rank of captain but was later tried at a court-martial for his conduct during the action of August 1702, and being convicted of cowardice and disobedience was executed by firing squad.
He had powerful relatives, including Arthur Herbert and Sir John Lowther, the latter being one of the Lords Commissioners of the Admiralty.
The first signs of his aversion to fighting were noticeable in an engagement against two French vessels (the Content and the Trident) on 18–19 January 1695 off Pantelleria.
Kirkby returned to England in 1698, where he was tried by court martial on charges of embezzlement and cruelty, accused of punishing a seaman for straggling by ordering him to be 'tied up by the right arm and left leg for several hours'[3] The board cleared him, but Kirkby did not receive another command and spent the next two years without a ship and on half pay.
Lowther was probably responsible for securing his return to active service, after Kirkby had written a number of letters pointing out this perceived injustice: And since their said Lordships have supplied the said ships with officers without respect to seniority or circumstance, there not being nine of the thirty one that are elder in command than I, and the rest being my junior officers, have most of them, if not all been paid off a considerable time, since the ship I lately commanded was discharged.
Over two dozen officers testified against him, stating that he had not encouraged his men to fight, but dodged behind the mizzenmast "falling down on the deck at the sound of a shot".
Kirkby wrote a letter to the Secretary of the Admiralty, Josiah Burchett, claiming that the defeat had instead been caused by Benbow's injudicious and ignorant conduct.
Kirkby was described as "very calm and easy, not railing or reviling, but forgiving all the world and praying, for the Queen's health and prosperity".