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Ignatian Rome: San Pietro in Vaticano

St. Peter's Basilica on Vatican Hill

beginning of 1547 the 71-year-old Michelangelo was placed in charge of the project. As construction advanced, the old basilica built by Constantine was gradually razed.
In the apse, to the left of the Altar of the Chair, is the tomb of Paul III who accepted the offering the first fathers made of themselves in 1538. Pierre Favre considered this event a memorable gift of God, and the foundation of the Society."
In the crypt are buried Popes Julius III del Monte (1550-1555) and Marcellus II (1555): both were most favorable to the young Society. Julius III approved the second Formula of the Institute and tried to provide the Roman College with a stable endowment. Marcellus II wanted to have two Jesuits with him in the Apostolic Palace. Ignatius designated Lainez and offered Pope Marcellus a list of four or five names from among whom he could choose the second. But his pontificate lasted only 21 days. His nephew Robert Bellarmine would enter the Society of Jesus in 1560.

Some historical vignettes:
St. Peter's was one of the Seven Churches visited by Ignatius the pilgrim in March-April of 1523. The companions made the same pilgrimage circuit in March-April of 1537; it was customary to begin at St. Peter's and go on foot to the other six. All of them went to St. Peter's on April 22, 1541, the day of their vows.
On March 6, 1544 Ignatius had a mystical experience here: "Having arrived at St. Peter's," he wrote in his Diary, "I began my prayer at the Altar of the Blessed Sacrament, a picturing to myself always in the same bright color the Divine Being Itself, such that within me there was no not seeing it. Afterwards, at the Mass (of Cardinal Cervini), in the same way the imaging in my mind and the seeing (came) with new mental feelings. After, from then to two o'clock, going to the same place of the Blessed Sacrament, and desiring to find the earlier experience, and seeking for it, there was no way."
The chapel where the Blessed Sacrament was reserved stood then near the present site of the Confession, i.e., near the high altar over St. Peter's tomb -- just about where the mosaic of Rafael's "Transfiguration" now stands.