In August 1685 Jeffreys opened at Winchester the commission known in history as the "bloody assizes," his conduct of which has branded his name with indelible infamy. The number of persons sentenced to death at these assizes for complicity in the duke of Monmouth's insurrection is uncertain. The official return of those actually executed was 320; many hundreds more were transported and sold into slavery in the West Indies. In all probability the great majority of those condemned were in fact concerned in the rising, but the trials were in many cases a mockery of the administration of justice. Numbers were cajoled into pleading guilty; the case for the prisoners seldom obtained a hearing. The merciless severity of the chief justice did not however exceed the wishes of James II.; for on his return to London Jeffreys received from the king the great seal with the title of lord chancellor. For the next two years he was a strenuous upholder of prerogative, though he was less abjectly pliant than has sometimes been represented. There is no reason to doubt the sincerity of his attachment to the Church of England; for although the king's favour was capricious Jeffreys never took the easy and certain path to secure it that lay through apostasy; and he even withstood James on occasion, when the latter pushed his Catholic zeal to extremes. Though it is true that he accepted the presidency of the ecclesiastical commission, Burnet's statement that it was Jeffreys who suggested that institution to James is probably incorrect; and he was so far from having instigated the prosecution of the seven bishops in 1688, as has been frequently alleged, that he disapproved of the proceedings and rejoiced secretly at the acquittal. But while he watched with misgiving the king's preferment of Roman Catholics, he made himself the masterful instrument of unconstitutional prerogative in coercing the authorities of Cambridge University, who in 1687 refused to confer degrees on a Benedictine monk, and the fellows of Magdalen College, Oxford, who declined to elect as their president a disreputable nominee of the king. Being thus conspicuously identified with the most tyrannical measures of James II., Jeffreys found himself in a desperate plight when on the 11th of December 1688 the king fled from the country on the approach to London of William of Orange. The lord chancellor attempted to escape like his master; but in spite of his disguise as a common seaman he was recognized in a tavern at Wapping--possibly, as Roger North relates, by an attorney whom Jeffreys had terrified on some occasion in the court of chancery--and was arrested and conveyed to the Tower. The malady from which he had long suffered had recently made fatal progress, and he died in the Tower on the 18th of April 1689. He was succeeded in the peerage by his son, John (2nd Baron Jeffreys of Wem), who died without male issue in 1702, when the title became extinct.