If you truly want to understand the history of Rome, then you have to look downwards.

This is a city that has grown haphazardly, in fits and starts, for thousands of years: a series of accretions encrusting the landscape like barnacles on the hull of an ancient galley. Each layer of Rome tells a unique story – of devastating floods and religious upheavals, of ambitious popes and new technologies. This is a city whose geography is its history.

By choosing to look, and eventually dig, down, we reveal the most important footsteps in the city’s timeline. The Renaissance itself was in a large part ushered into existence by the commitment of a handful of enlightened individuals to make a more concerted effort to observe what was occasionally revealed hiding in the ground beneath their feet; to look in depth at what the passing centuries had concealed, and to try to recreate it.

What they discovered was breathtaking. Every sculpture, every hidden building revealed a past so glorious that it had to be seen to be believed. Their curiosity of spirit has profoundly affected the ways in which Italians have interacted with their past ever since.

Today, more than 500 years after it started, the process of excavating Rome – amazingly – has really only just begun, and will never end. Every year thousands of new discoveries are made; each time the city authorities try to lay a new pipeline or upgrade the Metro system, substantial relics of the city’s past are exhumed from their earthen graves, forcing workers to down tools for months, or even years. It is no exaggeration to say that there are entire cities still lying below modern Rome, each one a single stratum of an ever-expanding geological puzzle.

This is a theme absolutely central to the city’s history, and yet one that is virtually unknown to the millions of visitors who come to Rome every year.

It is in the Basilica of San Clemente, hidden away in a quiet area of Rome not far from the Colosseum, where this unexpected journey through the sediment of history is perhaps most clearly and fully revealed. The church that today stands at the ground level of the city could hardly be considered modern: it was completed at the beginning of the 12th century, and the magnificently preserved mosaics within provide a jaw-dropping reminder of the skills of medieval artists. But walking into the cool, dark, 900-year-old church is only the beginning of our descent into the past here. Buried beneath this medieval basilica is another, far earlier church – one which dates back to at least the 4th century AD.

When the time came to create a new church for their congregation, those in charge of the basilica came up with a novel idea. Rather than move to a new site or destroy the beautiful-but-outdated 4th-century building, they would simply build on top of it, buried as it mostly was by silt from the annually flooding Tiber – and thus they inadvertently preserved at full height its murals, treasures, and ossuaries even while forgetting them. But it’s not just any church: in here is buried Saint Cyril, the man who brought Christianity to the Balkans, and gave his name to Cyrilic, the script he devised. Now fully excavated, we can be thankful for the original church-builders inadvertent foresight, an example of accidental conservationism from nearly a millennium ago.

Our journey doesn’t end here, though. Going down again under this church-under-a-church there is an even more rickety staircase, and at the bottom of that you are transported into the first century AD, the streets of Ancient Rome, and the earliest years of Christianity.

This was a time when to practice this new and obscure religion was still a criminal offence often harshly punished by Roman law.

Down an alleyway we find ourselves traversing a large building, training ground of gladiators, and private house, in all likelihood owned by one of the religion’s early converts. Christians could practice their faith here in relative security, hidden away from those passing by along the adjoining alleyway, which amazingly also survives intact beneath the church. The extravagance of the churches that were eventually be built above was a future that those secretly worshipping in this simple Christian temple could scarcely have imagined.

But Christians weren’t the only group using this area for worship. On the other side of the alleyway from the temple is the sacred space of another minority religious community: that of the cult of Mithras. This cave-like space embedded deep into the bedrock of the church evokes this cult’s mysterious nature. Banks of stone seating line the room, and in the centre stands an altar adorned with the cult’s most important image, that of the god Mithras slaughtering a bull.

The world of this ancient cult seems to be only very tangentially linked to our own, but it is in fact in these contested spaces that our modern world began to take shape: it could easily have been Mithraism that ‘won’ the battle of the cults, and its usurpation by the then-cult of Christianity in brings to light a moment of defining importance, not just in the development of Rome, but also of our modern world.

Historians typically go about their task chronologically, starting from the past and working their slow and methodical way towards the present day. In Rome, however, we must do exactly the opposite. In San Clemente in Laterano we can pick our way backwards from the modern city into a multitude of pasts, each more obscure than the previous, and as we descend we gain an unparalleled insight into the complex and unpredictable ways in which Rome came into being, and how has developed over the passage of the centuries.

This place is simply unmissable.