The following script is from "The Slave Ship" which aired on November 1, 2015. Scott Pelley is the correspondent. Nicole Young, producer.

Two hundred years ago, a ship named for St. Joseph, sank in a terrible storm. Half the passengers survived but the sea closed over more than 200 men, women and children who were locked below the deck. You would think a disaster like that would be legendary. But the St. Joseph was a slave ship. And the screams bursting from the hold were the cries of cargo.

Today, the silence of those lost voices is unbearable to Lonnie Bunch. He's the founding director of the Smithsonian National Museum of African American History and Culture, now under construction in Washington. Bunch found that to tell history the Smithsonian would have to make history. And, so began a quest for the remains of a shipwreck in a land so unchanged that an 18th century slave would recognize it today as the last shore he called home.

Mozambique Island defies the erosion of time. The Portuguese colonists who claimed it 500 years ago would still find the cut of the cloth that borrows the wind as familiar as the cut of the stone that framed their city.

Lonnie Bunch came to this capital of the slave trade because he was determined to launch America's new national museum on the remains of a ship.

Lonnie Bunch: I thought it wouldn't be hard. So I called museums around the world. And said, "OK, look, you must have some things. You must know where I can get some material." And everybody said, "Nope." And they said to me, "Well, Lonnie, almost every slave ship was at the end of its life, so it's probably at the ocean floor." And then I got scared. Then I thought, "Well, I'm not going to be able to find this."

Mozambique Island rises from the Indian Ocean, south of the equator. It was one of the points in what was called the Triangular Trade -- goods from Europe to Africa, slaves to the New World. And, cotton, gold and tobacco -- back to the old.

In the 1400s, the Portuguese were the first Europeans to trade in slaves and they became the largest, followed by the English, French, Spanish and Dutch. On Mozambique Island the Portuguese built a fortress that they called St. Sebastian for the Christian martyr who was captured, chained and murdered in Rome in the year 288. The irony of that name, was the only thing here the Portuguese failed to grasp.

Scott Pelley: You know, when you look at the enormous effort that went into building this fort they were protecting something that was hugely valuable to them.

Lonnie Bunch: They recognized that the key to their future as nations with economic prosperity was the slave trade.

St. Sebastian Fortress, Mozambique Island CBS News

The fort oversaw the trafficking of more than 400,000 slaves. Bunch was certain there had to be evidence of a ship and he soon discovered he wasn't the only one looking.

[Decio Muianga: Give me a hand.]

He found a group of researchers calling themselves the Slave Wrecks Project, and they were following a promising lead.

Scott Pelley: What do we find down here?

Decio Muianga: A very interesting thing.

Decio Muianga is a Mozambican archaeologist helping the Slave Wrecks Project locate the beginning of the story.

Decio Muianga: This is a tunnel that was used to put slaves inside the island or put them out of the island, as well.

Under the old Portuguese town, tunnels connected holding pens to the sea. The devout Portuguese preferred to keep slaves, in transit, out of sight.

Scott Pelley: How were these slaves captured?

Decio Muianga: Some individuals, African individuals, specialize in capturing slaves. So, they'll go and raid villages, far, far from here. And they walked, chained, all the way from there to here. And of course, lots of them died on the way.

Scott Pelley: So these were Africans capturing Africans?

Decio Muianga: It was not only a business for the Portuguese, the Europeans in this case, but also for the some of the local chiefs, as well.

Those local chiefs came to this auction house to sell captives to European clients.

Lonnie Bunch: A male in the late 18th century, early 19th century would go anywhere from $600 to $1,500, which is probably about, oh, $9,000 to $15,000 today.

Scott Pelley: This was incredibly lucrative.

Lonnie Bunch: In the years before the Civil War, the amount of money invested in slaves was more than the amount of money invested in railroads, banks, and businesses combined. This was the economic engine of Europe and the United States.

Lonnie Bunch: By the time you got here....

The enslaved marched from the auction down this ramp and on to the ships.

Lonnie Bunch: What you probably had was almost an assembly line. You'd bring people, you'd sell people. Then you would move them onto the boats and off to the New World.

Scott Pelley: What does black America need to hear, in your estimation, from the echoes off these steps?

Lonnie Bunch: I think all Americans need to recognize that, as tragic and horrible as slavery was, as big an economic shadow as it cast, the one thing it didn't do was strip people of their humanity. And I wish that all of us were as strong as the people that walked down those steps and got on those boats.

[Steve Lubkemann: We're wading out into the tidal flats...]

If Lonnie Bunch was to find his slave ship he would need Steve Lubkemann, co-founder of the Slave Wrecks Project. He's an anthropologist from George Washington University, who believes that slavery is the greatest story in maritime archaeology.

"I think all Americans need to recognize that, as tragic and horrible as slavery was, as big an economic shadow as it cast, the one thing it didn't do was strip people of their humanity."

Steve Lubkemann: Think about the way in which computers nowadays affect all of our lives. It's not just-- it doesn't affect just the computing industry. Everything is interlinked and depends on this. And the slave trade, in its time, was truly the equivalent. It reached into and influenced and created the modern world.

Even so, it's not likely much has survived centuries under the sea.

Scott Pelley: We're not talking about a hull that you're gonna find down there, and masts, and all of that, that you would imagine in your mind's eye?

Steve Lubkemann: We don't find intact ships. We find parts of ships. You have to go underneath the water, add some difficulty to this, find the pieces try to put them back together and put together the story that you can.

The story Lubkemann was searching for wasn't discovered underneath the water. His ship was lost in the dry, official records of Cape Town, South Africa -- which reach back to the 1600s. The Slave Wrecks Project had been diving into these binders for months when they discovered the St. Joseph, known in Portuguese as the Sao Jose.

The Sao Jose arrived at Mozambique Island in 1794. The cargo manifest records 1,500 iron bars for ballast and more than 400 slaves bound for Brazil.

"Bodies and souls laid side by side with no room to move, no sanitation. Many people on these voyages died."

This is a cargo sketch from a different, but typical, ship. Paul Gardullo is a historian of slavery and curator of the Smithsonian Museum.

Paul Gardullo: Bodies and souls laid side by side with no room to move, no sanitation. Many people on these voyages died.

Illustration of slaves treated as cargo

Scott Pelley: How long was that journey?

Paul Gardullo: A journey like the one the Sao Jose took would, could take up to four or more months.

Scott Pelley: This is slavery on a, global, industrial scale.

Paul Gardullo: From about 1500 through the 19th century, through late 1800, we're talking about at least 12 million people who were taken from their homelands across the sea, many, many hundreds of thousands more untold people were lost during that trade.

Off Cape Town, South Africa, the captain of the Sao Jose was caught between a violent storm and a nautical chart spiked with warnings: Whittle Rock, Bellow's Rock, Rocky Bank. The Sao Jose crashed, 212 slaves were killed. And because money had been lost there was an investigation. Interviews with survivors have survived.

Steve Lubkemann: This is the crew's account and right here we have the captain's account and he signed his name here, 220 years ago.

Scott Pelley: Incredible.

Steve Lubkemann: He said he decided, "to save the slaves and the people." The people are the crew. The slaves are just cargo.

The 200-year-old investigation pinpointed the site. And in 2010, divers responding to a metal detector, discovered bars of iron. One of those divers is Jaco Boshoff, an archaeologist with South Africa's Iziko Museum, and Lubkemann's partner in founding the Slave Wrecks Project. Boshoff says these are the iron bars, we mentioned a moment ago, on the Sao Jose Manifest, the ballast for the ship.

Scott Pelley: So you actually were excavating the sand on the sea bottom, this stuff was under the sand.

Jaco Boshoff: Under the sand.

Scott Pelley: So you're in how much water?

Jaco Boshoff: About five meters of water.

Scott Pelley: About 15-20 feet of water?

Jaco Boshoff: That's correct.

Scott Pelley: And then these are two feet under the sand below that.

Jaco Boshoff: That's right.

Turns out shallow water only makes the work harder. Surf tosses the divers. And sand, vacuumed away, settles back within hours. But, after more than 300 dives, this is what they've recovered so far. These are nails that pinned sheets of copper over the hull for protection. What looks like a lump of concrete is marine growth on a wooden pulley block -- similar to this one used to hoist sails and cargo. This X-ray shows the two white spaces where rope was threaded around the wheel. The divers discovered wood that a lab would later trace back to Mozambique. And, this, may be the most revealing artifact of all masked by two centuries under the sea, X-rays show a shackle, similar to this, used to bind slaves.

"The story of slavery is everybody's story. It is the story about how we're all shaped by, regardless of race, regardless of how long we've been in this country."

Jaco Boshoff: So there's a long bar running through. And shackles had-- often were on a long bar. The leg shackles especially.

Scott Pelley: So a long iron bar with a round metal ring?

Jaco Boshoff: That sort of thing, yes. And in this particular case, leg shackles.

Scott Pelley: Leg shackles?

Jaco Boshoff: That's right.

Scott Pelley: Have you found everything that's down there now?

Jaco Boshoff: No, not at all. Not, not even close. We've got a lot more to do. We've only scratched the surface at this stage.

Scott Pelley: How can you be sure that the wreck you found off Cape Town is, in fact, the Sao Jose?

Steve Lubkemann: There are certain types of artifacts that are found on this wreck that put us within a particular time bracket. Ceramics, for example. But then there are other things that I think are very important. We have an account that gives enormous specificity, in terms of geographic location, and it tells us the bay in which it was located. Finally, we find a document in Lisbon that says the Sao Jose's manifest, when it left Lisbon-- and the first item on that said, "1,500 bars of iron ballast." You put all of those different lines of evidence together, it's almost statistically impossible that it could be anything else.

They are the first artifacts known to be preserved from a ship on a voyage of slavery. And they will anchor the slavery exhibit, next fall, when Lonnie Bunch opens the National Museum Of African American History and Culture on the Mall in Washington.

Lonnie Bunch: The story of slavery is everybody's story. It is the story about how we're all shaped by, regardless of race, regardless of how long we've been in this country. We hope that we can be a factor to both educate America around this subject but maybe more importantly help Americans finally wrestle with this, talk about it, debate it, because only through that conversation can we ever find the reconciliation healing that I think we all want.