Nanni di Baccio Bigio managed to influence the deputies so that they appointed him Clerk of the Works instead of Pier Luigi, surnamed Gaeta, who was recommended by Michael Angelo in a letter( 168) to them.
Nanni then made a report, severely blaming Michael Angelo.

The Pope had an interview with the artist, and sent his relative, Gabrio Serbelloni to report on the works.

It was found that the irrepressible Nanni had again calumniated Michael Angelo, and he was therefore dismissed.
Notwithstanding the Pope's brief Michael Angelo's design was most seriously altered after his death by the erection of a long nave, making the ground plan a Latin instead of Greek Cross.

His idea appears to have been that people should enter the church up a majestic flight of steps through a gigantic door, and the hollow recesses of the huge dome should be the dominant impression as soon as the portal was passed.

To get his effect it is necessary to proceed half-way up the present nave with closed eyes, or merely looking at the pavement, the eyes religiously kept down.
Any one who will make this simple experiment (it is necessary to have a friend as guide to tell you when you have arrived at the right point of view) will see that Michael Angelo intended his building to have the effect of a coherent geometrical whole.