The next two years were busy ones. The president of St. John's, John B. Harley, was absent a great part of the time—first on fundraising tours for the new seminary, and then because of illness—and much of his work devolved upon Bayley. When in November 1845 Bishop Hughes took Harley with him to Europe in an attempt to restore his health, the full responsibility of carrying out the bishop's plans for St. John's fell upon Bayley. That winter, Bayley made a trip to Albany and secured a charter for St. John's from the New York State Legislature, granting them full university powers. In July 1846, Bishop Hughes transferred St. John's to the Society of Jesus, and Bayley was appointed to the parish in New Brighton, Staten Island, which included responsibility for a station once a month at Richmond and attendance at the large Quarantine Hospital given over then to victims of typhus.