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Parker chief author, and incurred in consequence a corresponding amount of unpopularity among the younger masters of arts, who were mostly favourable to puritanism, and who now made their appeal to Cecil. A series of objections was forwarded for the chancellor's consideration. Cecil referred them to Parker, who, in giving his opinion, denounced them as 'mere quarrels of envie against their rulers' (State Papers, Dom. Eliz. lxxxviii. No. 1). The new statutes accordingly passed into law. The relations between Parker and the university, in his latter years, were thus far from being altogether cordial. His devotion to its interests underwent, however, no diminution, and found expression in connection with other colleges besides his own. At the time that the contest respecting the new statutes was at its height, we find him pleading with Cecil that the endowment of Manchester College (then marked out for dissolution) might be settled on St. John's College, 'where you were brought up for the first beginning of your study' (Corresp. p. 365). But in little more than three months later (17 Aug. 1570) he lost his 'most beloved and virtuous wife,' whose remains were interred in the Duke of Norfolk's chapel in Lambeth; and for a considerable time after he laboured under severe mental depression. He roused himself when the tidings of the massacre on St. Bartholomew's eve (August 1572) reached England; and regarding, in common with many others, the captive Mary Queen of Scots as the real cause of the tragedy, he openly counselled her execution.

At Cambridge a fresh cause of trouble presented itself in the following year, when Thomas Aldrich, who had been promoted to the mastership of Corpus Christi on Parker's recommendation, espoused the puritan doctrines, refused to proceed B.D., and, on being censured by Burghley, resigned office in order to anticipate deprivation (, Hist. of College of Corpus Christi, ed. 1753, pp. 110-112). Of the now definitely organised puritan party Parker habitually spoke as 'irritable precisians,' while they in turn stigmatised him as 'the Pope of Lambeth.' His exercise of church patronage, which had hitherto been impartial and judicious, began to be directed almost solely with the view of checking the advance of the obnoxious doctrines; while, conscious of the strength of the opposing current, headed as it was by the all-powerful Leicester, and of the waning fidelity of not a few among his own order, he withdrew more and more from society, and went but seldom to court. In September 1573 he was, however, visited by the queen herself at Canterbury. His royal guest and her courtiers were splendidly entertained, and on their departure the archbishop presented Elizabeth with a massive gold salt-cellar, valued at over two hundred marks, while each of the courtiers received a copy of the volume 'De Visibili Monarchia,' designed as a reply to the malignant treatise of Nicholas Sanders [q. v.] Again, after the royal visit, his spirits sank. Writing to Burghley in the following November, he says: 'I have of late been shamefully deceived by some young men, and so I have been by some older men' (Corresp. p. 450). A year later he writes: 'I have little help, when I thought to have most. I toye out my tyme, partly with copieing of books, partly in devising ordinances for scholers to helpe the ministry, partly in genealogies and so forth' (, Life, Append. No. 95). He roused himself, however, to exercise his authority in ordering the discontinuance of 'prophesyings' in the diocese of Norwich, where puritanism largely prevailed. The privy council, under the influence of Sandys and Leicester, endeavoured to set the prohibition aside; but Elizabeth supported the primate, and the prophesyings were discontinued (ib. bk. iv. c. 37). In December in the same year his second son, Matthew, was carried off, at the age of twenty-three. His own health now began rapidly to fail; and, although his memory and mental faculties continued unimpaired to the last, 'the rheumatic Tempsis,' as he terms it, proved an effectual barrier to his passage over from Lambeth to attend the meetings of the privy council. He suffered acutely from the stone, and in March 1575 more alarming symptoms of the malady began to appear, to which he ultimately succumbed on 17 May following.

Parker was buried in his private chapel at Lambeth, where he had already caused his tomb to be placed; and his funeral, of which Strype has printed the 'order,' was honoured by a large and august following. An inscription, in Latin elegiacs, composed by Walter Haddon, was carved on the stone. This monument was, however, entirely destroyed in 1648, by the order of Colonel Scot the regicide, when Parker's remains were also disinterred and buried under a dunghill. After the Restoration Archbishop Sancroft caused them to be restored to their original resting-place, and composed an inscription, which he placed in the antechapel, recording both the act of desecration and the restoration of the monument.

Parker died wealthy; but his wealth and the means by which it was acquired have been the subject of much misrepresentation.