The year 1645-1646, during which Harvey held the office of Warden of Merton, was long a memorable one in the annals of Oxford. The City was invested by Fairfax for fifteen days from May 22nd, whilst the King was at Droitwich. On June 14th the Royal cause was ruined at Naseby, and on November 27th the College was called upon to lay in a supply of provisions against another siege. On December 28th the King ordered a special form of prayer to be used in the chapel on Wednesdays and Fridays "during these bad times." On March 24th the College gave a bond for £94 on account of provisions which it had no money to buy. At three in the morning of April 27th the King, disguised as a servant, with his beard and hair closely trimmed, passed over Magdalen bridge in apparent attendance upon Ashburnham and Hudson, and we cannot but believe that Harvey was one of the little band who closed the gates of the city with heavy hearts as his Majesty rode off to begin his wearisome captivity. On May 11, 1646, Oxford was summoned by Fairfax, and on June 24th it was surrendered on very honourable terms, the garrison marching out over Shotover 3,000 strong. The Duke of York fell into the hands of the Parliament; but Rupert, Maurice, and the greater part of the noblemen and gentlemen attendant upon the Court had left Oxford the day before its surrender. Mr. Brodrick says that "Harvey must now have retired from the Wardenship and Brent must have resumed office, though no minute of either event is preserved in the College Register." We find, however, that in September, 1648, Brent rendered accounts, as Warden, for the four years from 1642 to 1646.
Anthony Wood describes in language which has often been quoted, the utter confusion in which the past three years had left the University--the colleges impoverished, lectures almost abandoned, many of the students dispersed and others quite demoralised--"in a word, scarce the face of an University left, all things being out of order and disturbed." This account is confirmed by a striking entry in the College Register, under the date October 19, 1646, where it is stated that by the Divine goodness the Civil War had at last been stayed, and the Warden [Brent] with most of the Fellows had returned, but that as there were no Bachelors, hardly any scholars and few Masters, it was decided to elect but one Bursar and one Dean. It is also added that as the Hall still lay "situ et ruinis squalida" the College meeting was held in the Warden's lodgings.