The Great Pyramid of Cholula.
Under a 14th century Spanish Colonial church (a major pilgrimage destination) and covered with so much earth and other structures it looks like nothing more than a tall and regular hill lies a massive pyramid.
Begun somewhere around 200 BCE and built in stages over a thousand years, this elaborate pyramid complex is half a kilometer per side, larger in base and volume than the Great Pyramid of Giza, making it the largest monument in the world. Tunnels and passages wind through the structure; archaeologist have uncovered over six kilometers of passages so far. It is of course richly decorated, including fantastic murals, elaborate stone carving, and there are also multiple human burials.
And it is built on top of a cenote. Which, to add just that extra level of fantastic (something else I learned within the last couple of days) the distinctive cenote of Mexico's Yucutan Peninsula (deep circular pits where the surface has collapsed into massive limestone caves) are concentrated in a ring of shocked and fractured limestone that is itself a remnant of the Chicxulub Impact (the probable cause of the K-T extinction event of 68 MYA). These cenote are often connected in strings of caves, following the flows of an underlying aquifer which extends all the way to the sea.
Oh, yes, and just to put the Ancient Aliens firmly in the mix, an old name for the site is Acholollan (Nahuatl) meaning "place of flight." And, yes, the suggestion has been made that mysterious older inhabitants did just that. Perhaps their planet needed them.
So. Largely un-excavated (although quite well known and, like any ancient monument you've heard of, a major tourist destination), layered down through history from Spanish Colonization to late pre-contact to the height of the Mayan Empire to truly ancient caves to a catastrophe from tens of millions of years ago. Extending deep underground from the modern excavations to excavations by treasure hunters and seekers after building materials back through the Colonial age at least, to deep passages to natural tunnels to deep underground rivers stretching all the way to the sea.
And my only question is; why hasn't Lara Croft already been there to raid it?