In the upper right quadrant Nero sends St. Peter off to be executed (see detail).  A procession of soldiers conducts him to the place of execution in the upper left, where he is crucified upside-down (see detail).

In the bottom register the two pyramids and the taller structure between them are mausolea that stood along the street leading to what is now St. Peter's Basilica.  They were dismantled in the 7th century but continued to figure in some images of St. Peter's execution.  The flowing water that divides these structures from the main composition represents the Tiber. 

I have not identified the female figure to the right of the pyramid on the left (see detail).  The helmet suggests Minerva, but what would she be doing in this narrative?  And why do all those shields line the banks of the river?

More of St. Peter