For eighteen months (1587–8) he acted as Latin secretary to Cardinal Allen, and afterwards spent two years in Spain, and was with Father Parsons at his newly erected seminary at Valladolid.
He now declared that although he and his companion had been entrusted with treasonable commissions by Parsons, in preparation for a fresh attack upon England by the Spanish forces, they nevertheless detested all such practices, and had resolved to reveal them to the Government at the first opportunity.
For the next ten years this clever adventurer contrived, without serious difficulty, to combine the characters of a zealous missionary priest, a political agent of the Scottish Catholic earls in rebellion against the King, and a spy in the employment of Burghley and Sir Robert Cecil.
When George Kerr was captured, on his starting for Spain with the "Spanish Blanks", 31 December 1592, there were found among his papers letters from John Cecil to Cardinal Allen and to Parsons, assuring them of his constant adherence to the Catholic faith and of his sufferings in consequence, also a letter from Robert Scott to Parsons, referring indeed to some false rumours in circulation to the discredit of Cecil, but recommending him to the Jesuit on account of "his probity and the good service he had done in the vineyard".
To this Cecil, who had received about this time the degree of Doctor of Divinity from the University of Paris or of Cahors, replied in the rare tract, of which the copy in the British Library is probably unique; it is entitled A Discoverie of the errors committed and inivryes don his M.A.
At the end of 1601 Cecil was in France, and apparently in company with Robert Bruce; for Cardinal d'Ossat, writing from Rome, 26 November, warns Villeroi against both men as spies acting on behalf of Spain.
When the four deputies of the English appellant priests, John Mush, Bluet, Anthony Champney, and Barneby, were starting on their journey to Rome to lay before the Pope their grievances against the archpriest Blackwell and the Jesuits, Dr. Cecil unexpectedly took the place of Barneby in the deputation; and fortified with testimonials from the French government, in spite of D'Ossat's warnings, he for the next nine months assumed a leading part in the proceedings with the Pope and cardinals: proceedings in which one of the main charges brought against the Jesuits was their improper meddling with the affairs of state.
Parsons now in vain denounced Cecil to the Pope as a swindler, a forger, a spy, the friend of heretics, and the betrayer of his brethren; for as the Jesuit had made similar or more incredible accusations against all his other opponents, the charges were disbelieved or disregarded by the papal court.
He handed over, indeed, copies of certain letters touching Garnet to the English ambassador; but Carew, forwarding them to Salisbury, 2 February 1607, wrote that "he [Cecil] is of late so great with Père Cotton that I dare not warrant this for clear water".