The bishop was one of the most steadfast friends of Queen Mary. After the failure of the royal cause, and whilst Mary was a captive in England, Lesley continued to exert himself on her behalf. He was one of the commissioners at the conference at York in 1568. He appeared as her ambassador at the court of Elizabeth to complain of the injustice done to her, and when he found he was not listened to he laid plans for the escape of the queen. He also projected a marriage for her with the duke of Norfolk, which ended in the execution of that nobleman. For this he was put under the charge of the bishop of Ely, and afterwards imprisoned in the Tower of London. During his confinement he collected materials for his history of Scotland, with which his name is now chiefly known. In 1571 he presented the latter portion of this work, written in his own vernacular tongue, to Queen Mary to amuse her in her captivity. He also wrote for her use his Piae Consolationes, and the queen devoted some of the hours of her captivity to translating a portion of it into French verse.

In 1573 he was liberated from prison, but was banished from England. For two years he attempted unsuccessfully to obtain the assistance of Continental princes in favour of Queen Mary. While at Rome in 1578 he published his history De Origine, Moribus, et Rebus Gestis Scotorum, the Latinity of which is held only second to that of Buchanan. In 1579 he went to France, and was made suffragan and vicar-general of the archbishopric of Rouen by the Cardinal de Bourbon. Whilst visiting his diocese, however, he was thrown into prison, and had to pay 3000 pistoles to prevent his being given up to Elizabeth. During the remainder of the reign of Henry III. he lived unmolested, but on the accession of the Protestant Henry IV. he again fell into trouble. In 1590 he was thrown into prison, and had to purchase his freedom at the same expense as before. In 1593 he was made bishop of Coutances in Normandy, and had licence to hold the bishopric of Ross till he should obtain peaceable possession of the former see. Being tired of life, he retired at last to a monastery at Gurtenburg near Brussels, where he died in 1596.

The works of Lesley are as folloλvs :— A defence of the Honour of Marie Queue of Scotland, by Eusebius Dicaeophile, 8vo, London, 1569; A treatise concerning the defence of the Honour of Marie Qneene of Scotland, made by Morgan Ρhilip>pcs, bachelar of divinitie, 8vo, Liège, 1570-71; Pias afflicti animi consolationes, ad Mariam Scot. Reg., 8vo, Paris, 1574; Bro libertate impetranda Oratio, ad Elizabctham, 8vo, Paris, 1574; De origine, moribus, et rebus gestis Scotorum, libri deccm, 4to, Rome, 1578 and 1675; De illustrium foeminarum in republica administranda authoritate libellus, 4to, Rheims, 1580; De titulo et jure Marise Scot. Reg., quo regni Angliae successionem sibi juste vindicat, 4to, Rheims, 1580; A treatise touching the right of Marie Queens of Scotland, and of King James her graces sonne to the succession of the croune of England, 8vo, 1584; Congratulatio Alberto Archiduci Austrias de ejus adventu ad regimen provinciarum inferioris Germanies, 8vo, Brussels, 1596; The History of Scotland from 1436 to 1561, edited for the Bannatyne Club by Thomas Thomson from a MS. in the possession of the earl of Leven and Melville, 4to, Edinburgh, 1830. Several of Lesley’s works, of which the originals are very rare, will be found reprinted in Anderson’s Collections relating to the History of Queen Mary, and in Jebb, De vita Maries Reg. Scotorum.