The Ancient Ruins are a Labyrinth
The naive townsfolk think that they have found everything there is to know about this place, but they haven't even scratched the surface of what this complex really is.
The ignorant tomb raiders thought that this place only had one floor. They robbed the first floor until there was nothing left, never realizing that there was more beneath it.
This was intentional on the designer's part. They had lots of important items they wanted to keep hidden from prying eyes, and they were paranoid at the prospect that anyone would find them, so they set out to make the layout of this building as complicated as possible. They took the secret of how to navigate this place to their grave.
Despite looking like a simple structure at first, this building goes deep into the ground and has countless hidden tunnels as well, none of them in obvious places. They were so cleverly disguised that no one who passed by even realized there might be a secret path there in the first place. Why would they even bother to look?
This is the main reason why so many treasures remain unplundered and unsullied by mortal hands or eyes. Once the most important artifacts were stolen, people lost any interest in this place. They thought they mapped everything out and checked every corner, but they were only scratching the surface.
Not only are there more floors that they could have discovered, but there are dozens they have yet to touch. Thousands of rooms are lying hidden behind fake walls, secret trap doors, and tiny crawl ducts that no one ever bothered to check.
It's easy to miss this kind of thing, but the designer of this place wanted people to get as lost and disoriented as physically possible. They put all their hard work into concealing the truth.
Anyone smart enough to actually get into the more inner chambers of the building has found themselves way in over their heads. These areas were designed to be tough to enter and even tougher to exit. You might be able to open the doorway to Floor Two by sheer luck, but you'll never be able to get out without the proper code. You don't even need traps or monsters to guard the entrances and exits. An unbreakable stone wall blocking the way and endless caverns are enough. If you don't know what you're doing or where you are going, the entrance will lock behind you and you will be stuck in a lightless place until you eventually succumb to thirst or starvation, whichever comes first.
Just when you think the paths will come to an end, and you've finally found your way out, the maze just keeps going and going.
Exploring This Place Seems Futile
Why would anyone want to visit a place that has already been explored and has no treasure to offer?
This is one of the main reasons why people tend to stay away from it. They think it's already been pilfered, so what would be the point of going anywhere near it?
People tend to go exploring for two reasons. They either think there is something worthwhile in the location, or they are in it for the pure thrill of adventuring to an unknown place.
If there is no treasure left to steal, and the rumor that has been spread for years is that there is nothing good remaining, then no one would bother going there.
Have this building be protected by its sheer mundanity. As far as people are concerned, it has nothing left to give them. It's not an exciting destination to visit, it's a boring, dusty ruin that everyone wishes was demolished. It's just an eyesore.
It's called "hiding in plain sight". The more unassuming the place seems, the better hidden the artifact will be.
In fantasy, we tend to expect the McGuffin to be lying on a pedestal in some massive temple, surrounded by hundreds of powerful guards.
The guards might be a good idea, but if you really want to hide something, you wouldn't hide the McGuffin in someplace grand and luxurious. Hide it in a place so unsightly and boring it never occurred to anyone that it would be there.
Lots of Fakeouts and Lots of Fake Rewards
Have this be a reoccurring theme with this ancient civilization.
They love making people think they have found everything, all while they silently laugh in their graves because they know you walked out with something worthless compared to what was hidden a floor below you.
Like I was saying before, this place has dozens of floors underneath the main one.
The first one is designed to look like it is the only one, and countless valuable treasures are dotted along the place to make it more convincing.
Gold, silver, ancient weapons, and so on, are on every corner of the room and surrounded by traps, but all of that stuff is either a bunch of decoy goods or plain worthless compared to what this place was intended to hide.
This ancient civilization was rich. Gold, silver, and jewels were like dirt to them. Enchanted swords and spellbooks were everywhere. So they just shove all the worthless junk on the top floor to trick people into taking that. Once their greed is satiated and they find nothing else, they leave and think that is all.
Little did they know there were fire-shooting Gauntlets on the floor just below them. The designers laugh at the ignorance of the thieves.
Oh no, the thieves found the Fire Gauntlets? Sike. The real gauntlets were in another room. Those are fakes that scorch the user's bobdy until they're nice and crispy.
A hundred years pass and someone finally manages to find the real Fire Gauntlets on the Second Floor.
Jokes on them. On the Third Floor, they could have gotten the Elixir of Life which cures all illnesses and grants immortality. But they can keep their silly gauntlets.
Would you look at that? Someone found the Elixir of Life! Good for them. They have now cured all illnesses and ushered in a new era of peace. Good thing they didn't find the Dark Amulet on Floor 4 or else they might have unleashed the demon prince hidden within it.
Meanwhile, on Floor X, a ridiculous distance below the surface of the planet, the last remnant of the ancient civilization is snickering to herself.
The rest of her civilization transcended space and reality. That's why they all left, but she's decided to stick around and mess with adventurers like the main character until the day the sun dies and the world cools over. It's fun.
Ten thousand years after this place was built, she's bored. The main character is the first one to show interest in the Ancient Ruins for ages, so she (or he or they, you pick) decides to break radio silence and decides to give the main character a hint of what is truly hidden beneath the surface.
This could be how the crux of the story begins. The character takes interest in these seemingly boring and mundane ruins, gets a hint from an outside force, and investigates to find there was far more to this place than anyone ever knew. They unveil secrets that have never seen the light in millennia.