Their object was to open up communications with Esmé Stewart, 1st Duke of Lennox, procure the conversion or deposition of the young James VI, and send information to Mary and Philip II of Spain through the Spanish ambassador Mendoza.
But James VI soon took him into his own hands, and ordered him to be imprisoned in Edinburgh Castle, while Elizabeth demanded his surrender as an English subject, and asked that he should be put to torture and compelled to confess.
In 1585 he returned to Scotland to work on behalf of Mary, and was harboured by George Gordon, 6th Earl of Huntly in the north, In 1586 Holt was summoned to Rome and made rector of the English College, a post which he held for a year and a half, when in 1588 he was transferred to Brussels, to act as agent for Philip II, and direct the political activity of the English exiles.
Edmund York, who was executed for high treason in 1595, is said to have confessed that Holt promised him forty thousand ducats if he would murder the queen, and the statement was repeated at Robert Southwell's trial; likewise Patrick O'Collun, executed for treason in 1594, said that Holt had promised him a generous pension and granted him absolution for killing the Queen.
Representations against Holt were made to Pope Clement VIII, who said to Barret, "Accepi nuper litteras ex Belgio de quodam patre qui ibi dominator et tyrannizat".
The question was referred to the Cardinal Archduke Albert, and by him committed to the father provincial for Germany, Oliver Manareus and Don Juan Battista de Tassis.
The only writing of Holt which is preserved is a memoir Quibus modis ac mediis religio Catholica continuata est in Anglia, published by Knox, Douay Diaries, pp. 376–384.