Now, one of the greatest undersea explorers in the world, Robert Ballard, is trying to uncover their secrets. You may know him as the man who discovered the Titanic, but what he couldn't say then is that he was on a clandestine mission for the Navy at the time. It was a secret he kept for more than two decades until the mission was declassified.
You'll hear how that mission helped him find the most famous wreck in modern history and about Ballard's many other discoveries in his 50 years at sea.
National Geographic: Ocean Now
Web Extra: Trapped!
Web Extra: PT-109
Web Extra: Finding Titanic
Web Extra: Echoes of the Past
When Ballard took "60 Minutes" and correspondent Lara Logan with him to hunt for ancient shipwrecks off the coast of Turkey, we made an extraordinary find even he didn't expect.
To get to Ballard, we had to make a journey of our own to what used to be one of the great crossroads of civilization.
For thousands of years, ancient mariners passed through beautiful but treacherous waters to the place where the Aegean Sea meets the Mediterranean. Many of them didn't make it, their ships sinking deep below, as far as 2,000 feet down, never to be seen again.
That's where we found Ballard.
His ship, the Nautilus, never sleeps. Ballard and his team had been out there for two weeks hunting for shipwrecks - a 17-man crew of archaeologists, scientists and engineers working in shifts around the clock.
"We're here to find lost chapters of human history, chapters we've never read before," Ballard told Logan.
Asked how many shipwrecks are down there, Ballard said, "In this area, I'm sure there's hundreds if not thousands along this coast."
Shipwrecks that have never been seen.
The Nautilus is specially designed for deep sea exploration, armed with state-of-the-art electronics and navigation systems. Ballard's team uses sophisticated underwater sonar to guide them to possible wreck sites, called "targets."
On a monitor, the targets appear as little dots.
"But you can sort of start to figure it out because they have shadows. So if a ship went by like the Titanic, you'd get a very big target but then you'd have a very large shadow because it's a hundred feet above the bottom. What we're looking for is not the Titanic. We're looking for literally a needle in a haystack. We're looking for very small ancient ships," Ballard explained.
Once Ballard has a target worth exploring, he sends down what he calls, his "big guns": two remote controlled vehicles, his eyes under the sea.
They descend thousands of feet to the target, using high definition cameras and powerful search lamps to shed light on a place that has always been in darkness.
The drama of the hunt plays out in Ballard's command center aboard the Nautilus.
His team is particularly interested in what they think is a wreck that they spotted with the sonar. The crew is glued to the screens.
Pilots guide the remote controlled vehicles towards the target, some 1,500 feet below.
Asked what he thought he might find, Ballard told Logan, "I have my fingers crossed that it's an ancient shipwreck."
In the back of the room, archeologists stand ready to tell Ballard what he may have found. This is the moment of discovery that still thrills Ballard after half a century at sea.
"And the anticipation, 'What is it?' Don't know. And you come in, and you come in, and you think, 'Well, it could be this. It could be…' And then all of a sudden, the veil of darkness in the deep sea, like curtains, just open, and there it is. And you see it for the first time for 2,000 years, or whatever. You can get used to that," Ballard said.