After hearing Bacon's bold claim that all of education needed to be revised, and that the revisions could be found in his work, Pope Clement IV demanded to see the documents. Bacon had been misunderstood: what he had meant was that he could write such material, not that he already had written it. He was bound by a papal oath of secrecy, and composed without the knowledge of his superiors a three volume encyclopedia on the sciences.

Even during his life as a Fransiscan, Bacon remained very involved in the sciences: he published a good deal of work on logic, the experimental sciences, etc. until Jerome of Ascoli (the Minister General of the Fransciscans) condemned his work due to "suspect novelties" they contained. Bacon appealed to the pope and lost. After serving two years in prision, Bacon began work on his final publicatoin: a scathing crticism of Christianity's corruptness. It was published the year of his death.