In the fall of 1841, Bayley resigned his rectorship, and his grandfather, alarmed at his evident inclination for the Catholic religion, decided to send him to Rome, hoping that what Roosevelt considered the corruption and superstition to be seen in Rome would disabuse Bayley of his attraction to Rome's religion. Father McCloskey gave Bayley advice about travelling to Rome and two letters of introduction, probably addressed to the rector of the Pontifical Irish College, Paul Cullen, and the rector of the English College, Dr. Baggs. On the morning of December 8, his father and two of his brothers, Carleton and William, accompanied him to the wharf where he boarded the packet ship "Emerald", bound for Le Havre. The three weeks' voyage was uneventful except for severe seasickness, from which he suffered the first week. One heavy gale was encountered during which the ship was obliged "to lay under storm-sails."