He was chosen rector of the university of Paris on 17 Oct. 1584 (Bulæi Hist. Univ. Paris. vi. 785). In the following year he was commended by the students forming the German nation to the cure of the parish of St. Côme (ib. p. 786). His title was disputed before the parliament of Paris, but was decided in his favour (ib.). One of the objections to him was that he could not speak Latin nor French, but Louis Servin, his advocate, asserted that he was ready to prove his knowledge of both. He was then only a student in theology, and did not become master till 1586.
Hamilton became one of the most prominent members of the Catholic League, especially during the resistance to Henry IV. He wrote a preface, dated from ‘Saint Cosme’ on the last day of March, to ‘Remonstrance faicte en l'Assemblée Générale des Colonnels, Cappitaines, Lieutenans & Enseignes de la Ville de Paris,’ by Monsieur de Saint-Yon, 1590. When Henry besieged Paris the curé of St. Côme acted as adjutant, or sergeant-of-battle, of the thirteen hundred ecclesiastics who on 14 May 1590 were reviewed in ‘belle ordonnance’ (L'Estolie, iv. 24). Sometimes he made them halt and sing hymns; anon he commanded them to march, and then to give fire (ib.). Hamilton was one of the representatives of the Sixteen of Paris who offered the crown to Philip II of Spain. The society also decreed the death of Brissot, president of the parliament of Paris, and of L'Archer and Tardif, two of the councillors. When Tardif could not be found Hamilton went out to seek him, and, discovering him ill in bed, dragged him as he was to the execution chamber. Hamilton is stated to have said mass frequently in his cuirass, and to have baptised an infant in full church without taking off his armour. When Henry entered Paris in 1594 Hamilton was apprehended with a halbert in his hand about to join the band of fanatics who gathered to resist the entrance of the king, but though the other ringleaders were executed, he succeeded in making his escape, and retired to Brussels. In his absence he was condemned to be broken on the wheel for the murder of Tardif, and the sentence was executed on his effigy. About 1600 he and Edmond Hay the jesuit [q. v.] returned to Scotland, apparently on a secret proselytising mission. In 1581 Hamilton had published at Paris ‘Ane Catholik and Facile Traictise, Drauin out of the halie Scriptures, treulie exponit be the ancient doctores, to confirme the real and corporell praesence of Chrystis pretious bodie and blude in the sacrament of the alter.’ It was dedicated to Queen Mary, and appended to it were ‘twenty-four Orthodox and Catholic conclusions’ dedicated to James VI, containing ‘Certan Questions to the quhilks we desire the Ministers mak resolute answer at the next General Assemblie.’ This letter was answered by William Fowler (fl. 1603) [q. v.] It was probably as preparatory to his return to Scotland that he published at Louvain in 1600 ‘A Facile Traictise, contenand, first: ane infallible reul to discerne trevv from fals religion: Nixt a declaration of the Nature, Numbre, Vertevv and effects of the Sacraiments: togider vvith certaine Prayers of deuotion. Dedicat to his Sovereain Prince the kings Maiestie of Scotland, King Iames the Sext. Be Maistre Ihone Hamilton, Doctor in Theologie in Brussels.’ Burton says that Hamilton ‘had that subtle gift, the empire over language; and the words came to him at his bidding,—words expressive of Christian meekness, humility, charity, and all that might seem more appropriate to the secluded anchorite than to the man of storm and strife.’ This is undoubtedly true of Hamilton's prayers, but his controversial writings are chiefly notable for the wild extravagance of their calumnies against the reformers, and the gravity with which extraordinary stories are related of their commerce with the devil. On 24 Nov. 1600 a proclamation was issued by the king and council against Hamilton and Hay (Reg. P. C. Scotl. vi. 172). On 22 June 1601 an act was passed against resetting them, but for several years they not only succeeded in eluding capture, but even in holding frequent meetings in different parts of the country for the celebration of the mass and other catholic services. His escape was probably procured by his nephew, Thomas Hamilton, first earl of Haddington [q. v.], who was then practically at the head of the justiciary of Scotland, and whom Andrew Melville to his face accused of screening him (M'Crie, Life of Melville, 2nd ed. ii. 146–7). He was, however, finally captured in 1608, for on 30 Aug. of that year Sir Alexander Hay desired the lieutenant of the Tower to receive two priests, Hamilton and Paterson, sent by the Earl of Dunbar (Cal. State Papers, Dom. Ser. 1603–10, p. 454). Calderwood wrongly gives the year of his capture as 1609. Hamilton died in prison, but the date has not been ascertained.
[L'Estoile's Journal de Henry IV; Bulæi Hist. Univ. Paris, tom. vi.; Launoii Opera Omnia, tom. iv. pt. ii.; Hist. of James the Sext (Bannatyne Club); Richard Bannatyne's Memorials; Reg. P. C. Scotl. vols. ii. and iv–vi.; Calderwood's Hist. of the Church of Scotland; Francisque-Michel's Les Écossais en France, ii. 117–122; Sketch of the Life of John Hamilton by Lord Hailes; Sir William Fraser's Earls of Haddington.]