He had been firmly of the position that Catholicism and its claims were both false and treasonable, however, while visiting a Catholic friend, he began casually flicking through a book of theology and was struck by the force of an argument he read there.
This caused him to enter into a period of intensive study and prayer, and it was only after two years of intellectual and spiritual struggle that he finally decided to be received into the Catholic Church.
Scott was to be taken to Valladolid, Spain for his monastic formation in the Lent of 1604, but on attempting to leave England, he was arrested along with Roberts and a group of other postulants on suspicion of being Catholic.
However, this arrest proved only a temporary delay, as immediately after his release he was taken to Valladolid by Augustine Bradshaw, where it was agreed that he should serve his novitiate at the Abbey of San Facundo, Sahagún.
However, this was not accepted and Scott was placed in close confinement (although not before drawing on his legal expertise to insist that Abbot did not have jurisdiction to hand down such a punishment).
He then addressed the people in the court, explaining that the only reason that he had not yet confessed himself as a priest was to see if the law would take its course, or whether he would be condemned on presumption of guilt without any proof.
He appeared wearing his Benedictine habit and declared himself once again a loyal subject of the King, before being tied to a horse and dragged through the streets to the gallows at Tyburn.
Before being executed, he made a declaration of his life, his faith and his conversion to the Catholic Church, and gave the small number of gold coins he had in his purse to the executioner, saying, "Take these, friend, for love of me.