The See of Orkney became vacant by the death of Robert Reid at Dieppe, 6 September 1558, on his way home after attending, as a commissioner, the marriage of Mary, Queen of Scots with Francis the Dauphin.[3] At the Edinburgh meeting, memorable for the first communication (on a case of restitution of conjugal rights) addressed by the assembly to the English archbishops, Bothwell was made one of the commissioners for revising the Book of Discipline.They decided inter alia that no minister should be a pluralist unless able personally to discharge the accumulated duties, and 'providing he be sufficiently answered of one stipend,' a rather ambiguous loophole.Calderwood says that 'the Bishop of Orkney, at the marriage, made a declaratioun of the Erle of Bothwell his repentance for his former offensive life; how he had joined himself to the Kirk, and embraced the reformed religioun;' he adds, 'but they were married the same day, in the morning, with a masse, as was reported by men of credite.'"[3] Mary's abdication soon followed, on 24 July; and on the 29th, at Stirling, her son (born 19 June 1566, baptised "Charles James" 17 December, according to the Roman rite) was crowned and anointed by the Bishop of Orkney.However, on 10 July 1568, the assembly restored him to the ministry, did not renew his commission to superintend the diocese of Orkney; but ordered him, as soon as his health permitted, to preach in the Chapel Royal ("kirk of Halyrudhous"), and after sermon confess his offence in the matter of the ill-fated marriage.In 1570, he exchanged the greater part of the temporalities of the See with Robert Stewart, natural brother to Queen Mary, for the abbacy of Holyrood House.He claimed in his defence to the assembly in March 1570, that "Lord Robert violentlie intruded himself on his whole living, with bloodshed, and hurt of his servants; and after he had craved justice, his and his servants' lives were sought in the verie eyes of justice in Edinburgh, and then was constrained, of meere necessitie, to tak the abbacie of Halyrudhous, by advice of sundrie godlie men".The result of their labours 'is remarkable,' says Grub, 'for its general resemblance to the external polity of the Church, as it existed before the Reformation in Scotland, and as it was at that time sanctioned by law in England.'Four years passed, and in October 1582 the general assembly appointed Andrew Melville and Thomas Smeaton to confer with the bishop of Orkney on his having ceased from the exercise of the ministry.Appended to his epitaph, on a tablet fixed to the third south pillar from the east end, are some fulsome elegiacs, subscribed M. H. R. (Master Hercules Rollock).[3] He married Margaret, daughter of John Murray of Touchadam, by whom he had: Adam Bothwell's house still exists, north of the Royal Mile in Edinburgh's Old Town, accessed from Advocates Close to its east.