When Henry besieged Paris Hamilton acted as adjutant, or sergeant-of-battle, of the thirteen hundred ecclesiastics who on 14 May 1590 were reviewed in good order.
When Henry entered Paris in 1594 Hamilton was apprehended with a halberd in his hand about to join those resisting the king; but though the other ringleaders were executed, he succeeded in escaping to Brussels.
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.
He was, however, finally captured in 1608, and on 30 August of that year Sir Alexander Hay desired the lieutenant of the Tower of London to receive two priests, Hamilton and Paterson, sent by the Earl of Dunbar.
In 1581 Hamilton 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 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.