And disbelievers can explain away the other clues. The Bernini sculptures were modeled after the niece of the pope; the Vicus Papissa was named for a woman who lived in the area.
Yet even those who laugh at the story of the female pope agree that it opens a window on the history of women and sex in the Catholic Church. Women were at one time a potent and threatening force in the medieval church.
Many scholars say there were many women martyrs in that era, women who were tortured for their religious beliefs. And there were women who became saints while cross-dressing as monks.
St. Eugenia, for example, became a monk while disguised as a boy, and was so convincing she was brought to court on charges of fathering a local woman's child. She finally proved her innocence only by baring her breasts in public.
"There are over 30 saints' lives in which women dress as men for a variety of reasons, and with a variety of outcomes," says Hotchkiss, who has written about these "transvestite nuns."
Perhaps most threatening to the church were two groups of women known as beguines and mystics, who claimed they could bypass the church hierarchy and communicate directly with God.
"And they really terrified the church because they went around saying things like 'My real name is God,'" says Malone. "And so mysticism, then, gave these women ... an access to God that was parallel to the church."
These powerful women could have inspired a so-called crackdown by the church after A.D. 1000, as it consolidated its ranks and reaffirmed the rules on celibacy among its priests, a requirement that's still controversial today.
One school of thought says the story of Pope Joan was invented as a cautionary tale. The lesson to women: Don't even think about reaching for power or you will end up like her -- exposed and humiliated.
Another school argues that it was the fear of female power that led the church to essentially expunge Pope Joan from history.
But how do historians explain the enormous purple marble chair on which popes once sat as they were crowned. The chair has a strange opening, something like a toilet seat, reportedly used to check "testiculos habet" -- or whether the pope had testicles.
David Dawson Vasquez, the director of Catholic University of America's Rome program, says that the Vatican was just using the most impressive chair it had.
"Because it's elaborate, it's purple. It was the most expensive marble of Roman times, and so it was only used for the emperor," Vasquez says. "The hole is there because it was used by the imperial Romans, perhaps as a toilet, perhaps as a birthing chair. It doesn't matter if there's a hole there, because you can still sit there and be crowned."
Others say it was a symbol of the pope giving birth to the mother church. Either way, newly minted Protestants in the 1500s had a field day making fun of the chair, and so it was hidden from view.
And so the last relic in the tale of Pope Joan is withdrawn. But Pope Joan lives on in some other place, in the shadows of a Dark Ages legend that is terrifying to some and inspiring to others.