A pope ordered secret excavations under his own basilica looking for a burial spot for himself, and instead uncovered an entire ancient cemetery nobody expected to find intact.
Five architects, one building
Construction of the current basilica spanned more than a century, passing through the hands of successive architects including Bramante, who established the initial design, Raphael, Michelangelo, who designed the great dome, and finally Carlo Maderno and Gian Lorenzo Bernini, whose bronze baldachin over the high altar and sweeping colonnade in the piazza outside completed the building's most recognisable features, a genuinely multi-generational architectural project rather than a single coherent commission.
An accidental cemetery beneath the altar
Pope Pius XII ordered excavation beneath the basilica in the 1940s, reportedly seeking a suitable burial location for himself, and the resulting dig instead uncovered an extensive ancient pagan and early Christian necropolis directly beneath the high altar, a discovery considerably larger and more significant than the modest burial arrangement the excavation had originally been commissioned to find.
As this entry's companion article covers
The specific bones found within that necropolis, and the Vatican's disputed 1968 announcement identifying them as the remains of Saint Peter himself, are addressed directly in this entry's companion article rather than repeated here.