Hutchinson, in his History of Massachusetts, analyzed the trouble as follows:
"Sir William Phips' rule was short. His conduct when captain of a ship of war is represented very much to his advantage; but further talents were necessary for the good government of a province. He was of a benevolent, friendly disposition; at the same time quick and passionate....
"A vessel arrived from the Bahamas, with a load of fustick, for which no bond had been given. Col. Foster, a merchant of Boston, a member of the Council, and fast friend of the Governor, bought the fustick at such price that he was loth to give up the bargain. The Collector seized the vessel and goods; and upon Foster's representation to the Governor, he interposed. There was at that time no Court of Admiralty. Sir William took a summary way of deciding this case, and sent an order to the Collector to forbear meddling with the goods, and upon his refusal to observe orders, the Governor went to the wharf, and after warm words on both sides, laid hands upon the Collector, but with what degree of violence was controverted by both. The Governor prevailed, and the vessel and goods were taken out of the hands of the Collector.
"There had been a misunderstanding also between the Governor and Captain Short of the Nonesuch frigate. In their passage from England a prize was taken; and Short complained that the Governor had deprived him of part of his share or legal interest in her. Whether there were grounds for it does not appear. The captains of men of war stationed in the colonies were in those days required to follow such instructions as the governors gave them relative to their cruises and the protection of the trade of the colonies, and the Governor, by his commission, had power in case of any great crime committed by any of the captains of men of war, to suspend them, and the next officer was to succeed.
"The Governor required Captain Short to order part of the men belonging to the Nonesuch upon some service, which I do not find mentioned, probably to some cruiser, there being many picaroons about the eastern coasts, but he refused to do it. This was ill taken by the Governor; and meeting Captain Short in the street, warm words passed, and at length the Governor made use of his cane and broke Short's head. Not content with this, he committed him to prison. The right of a governor to commit by his own warrant had not then been questioned.
"From the prison he removed him to the castle, and from those on board a merchant bound to London, to be delivered to the order of one of their Majesties' principal secretaries of state; giving the master a warrant or authority to do so. The vessel, by some accident, put into Portsmouth in New Hampshire. Sir William who seems to have been sensible of some irregularity in these proceedings, went to Portsmouth, required the master of the merchantman to return him the warrant, which he tore to pieces, and then ordered the cabin of the ship to be opened, secured Short's chests, and examined the contents.
"Short was prevented going home in this vessel, and went to New York to take passage from thence for England; but Sir F. Wheeler arriving soon after at Boston, went for him and carried him home with him. The next officer succeeded in the command of the ship, until a new captain arrived from England. Short was restored to the command of as good a ship."
King William refused to depose the famous treasure finder without hearing what he had to say in his defense, and Sir William stoutly swore that those whom he had punished got no more than they deserved. A strong party had been mustered against him, however, and he waged an uphill fight for vindication until Death, the one foe for whom he did not think himself a match, took him by the heels and laid him in a vault beneath the Church of St. Mary Woolnoth, London. A guide-book of that city, published in 1708, contained this description of the memorial placed therein:
"At the east end of the Church of St. Mary Woolnoth, near the northeast angle, is a pretty white marble monument, adorned with an urn between two Cupids, the figure of a ship, and also a boat at sea, with persons in the water; these beheld by a winged eye, all done in basso relieve; also the seven medals, as that of King William and Queen Mary; some with Spanish impressions, as the castle, cross-portent, etc. and likewise the figures of a sea quadrant; cross-staff, and this inscription:
"'Near this place is interred the Body of Sir William Phips, knight; who in the year 1687, by his great industry, discovered among the rocks near the Banks of Bahama on the north side of Hispaniola a Spanish plate-ship which had been under water 44 years, out of which he took in gold and silver to the value of £300,000 sterling: and with a fidelity equal to his conduct, brought it all to London, where it was divided between himself and the rest of the adventurers. For which great service he was knighted by his then Majesty, King James the 2nd, and at the request of the principal inhabitants of New England, he accepted of the Government of the Massachusetts, in which he continued up to the time of his death; and discharged his trust with that zeal for the interests of the country, and with so little regard to his own private advantage, that he justly gained the good esteem and affection of the greatest and best part of the inhabitants of that Colony.