Between 1532 and 1534, Michelangelo divided his time between Rome and Florence, but he had already decided to settle permanently in Rome. In Florence, he continued work on the Medici Chapel, and he oversaw the construction of the wooden elements of the Biblioteca Laurenziana, which was not completed until 1559. After his final move to Rome, Michelangelo entrusted the completion of the Chapel project to assistants. In 1533, Michelangelo did more work on the tomb of Julius, and in 1534 Pope Clement VII commissioned him to paint a Resurrection scene on the altarpiece wall of the Sistine Chapel, thereby finishing the Sistine project and finally fulfilling the contract promised by Pope Julius II twenty years earlier. The subject of Christ's Resurrection was a particularly appropriate topic, allowing the Pope to make an important statement about the enduring strength of the Catholic church in spite of the 1527 Sack of Rome and the Protestant Reformation.
After this time, Michelangelo remained in Rome until his death, despite frequent solicitations from Cosimo de'Medici, whom he despised, to return to Florence. Clement VII died in 1534, and his successor, Paul III, urged Michelangelo to continue with the Sistine altarpiece fresco. Paul III changed the subject, however, from the Resurrection of Christ to the Last Judgment. Paul also forbade Michelangelo from continuing work on the tomb of Julius, so Michelangelo had to work on it in secret, with substantial help from assistants.
Michelangelo began work on the Last Judgment in the spring of 1536, finishing five years later, in 1541. The whole while, he was hurried and pestered by Pope Paul III. The Last Judgment is remarkable for its incredibly complex composition and spatial organization. The central figure of Christ controls the entire wall, controlling the anguished figures' spiritual destinies as if they were puppets. This violent vision of the final division between salvation and damnation was extremely influential in later depictions of the subject, and the fresco's dark tone indicate that Michelangelo may have been feeling sexual guilt and a certain sense of foreboding. The issues of mortality and personal salvation were central to the artist's later art and particularly to his poetry, to which he turned more and more at the end of his life. The shift in his interest from the sensual Classicism of Neoplatonism to a more austere version of Christianity was due in part to the influence of the Reformation and its emphasis on personal salvation and justification by faith.
I think the time when the Council of Trent condemned naked pictures was in Session XXV on December 4,1563. The public domain translation of the Council of Trent by Tanner says, "Furthermore, in the invocation of the saints, the veneration of relics, and the sacred use of images .... all lasciviousness avoided, so that images shall not be painted and adorned with a seductive charm"