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STEVE INSKEEP, host:

This is MORNING EDITION from NPR News. I'm Steve Inskeep.

Some historians want to find a Navy vessel that's been missing for more than a century. The USS Alligator was an early submarine. The Union Navy built it during the Civil War. It was an iron tube less than 50 feet long designed to sneak under enemy ships so that a diver could plant explosives. But the Alligator never fought before disappearing in 1863. Today, the search for the Alligator took NPR's Nell Boyce to the waters off North Carolina.

NELL BOYCE reporting:

The USS Alligator looked like something right out of Jules Verne. She was so small that crew members had to crouch inside. Her propeller was turned by hand. She's rarely mentioned in history books, but she was Abraham Lincoln's secret weapon built to sink the Confederacy's dangerous new ironclads. She was on her way to attack the port at Charleston, South Carolina, when the weather turned ugly. Michael Overfield works for the National Oceanic and Atmospheric Administration.

Mr. MICHAEL OVERFIELD (National Oceanic and Atmospheric Administration): They had to cut her free so she wouldn't sink the USS Sumter, which was a ship that was towing her.

BOYCE: And so they cut her free and then what happened? Did they see her go down?

Mr. OVERFIELD: We don't know what happened. They lost sight of her. So they don't know whether she sank right away or if she floated for a while in the gulf stream.

BOYCE: Overfield is chief scientist in the government's search for the Alligator, which was the first underwater craft to have all kinds of innovations found on modern subs. The search is a long shot. If the Alligator floated, she could be anywhere. But Overfield's team think she sank fast, and they think they know where.

(Soundbite of ship's horn)

BOYCE: We're headed to the spot 30 miles off Ocracoke Cove, North Carolina, aboard an Office of Naval Research ship. Experts have used historical documents and computer models to re-create the Alligator's last moments. They think she's somewhere in this 150-square-mile chunk of ocean. We arrive at a site that scientists have previously scanned with sonar. Those images showed about a dozen intriguing features on the bottom, 250 feet down.

(Soundbite of background talking)

BOYCE: The researchers want to check them out with a device that looks like a small torpedo. It's a magnetometer. It measures magnetic fields to detect hunks of metal. Richard Dentzman works for a company called iXSea. He says this one is so sensitive, it can spot all kinds of things.

Mr. RICHARD DENTZMAN (iXSea): Locate car engine blocks, washers, dryers, refrigerators. In this area, we'll probably see a lot of things. There's a lot of wrecks out here.

BOYCE: The crew lowers the magnetometer over the side. It looks like a big, yellow fish caught on a line, then sinks out of sight.

Unidentified Man: ...in the water anytime you want.

BOYCE: The ship drags it back and forth. Ten men gather inside the rocking boat to stare intently at a thin green line that wiggles across the computer screen. Everyone is silently waiting for a big spike that means metal.

(Soundbite of background talking and ship equipment moving)

BOYCE: They do this for two hours. It's like the world's most boring video game. Eventually, a grim humor sets in and Overfield jokes about throwing metal overboard just so they can see something. The ship heads towards the last target of the day.

Mr. OVERFIELD: Inevitably, you spend an entire day doing survey and you don't find anything until the last three minutes of the survey. That's why I'm saving this one, so we can just go right over that and we'll have a big spike and a big hurray.

BOYCE: That doesn't happen. As the ship heads home, the crew wonders if the probe was close enough to the sea floor. Overfield says people love to blame the equipment.

Mr. OVERFIELD: It's generally not the equipment. It's just generally--it's generally there was nothing there, and we just find it hard to believe.

(Soundbite of ocean waves)

BOYCE: Dark clouds start to gather and the wind picks up.

(Soundbite of sea gulls)

BOYCE: Hurricane Ophelia is threatening the rest of the mission and it could be months before they're able to search again. Still, another ship that went out today will give the team thousands of new sonar images to sort through, and Overfield says looking for this lost piece of history is a far better gig than his previous career: managing hotels and sitting at a desk.

(Soundbite of background talking)

Mr. OVERFIELD: As long as there's a challenge to be had, I'm in the game. I don't give up easy, you know. That needle-in-the-haystack search, you'll never find the needle if you don't look. And a lot of people just look at that stack and they say, `I'm not willing to put in the time and effort to find that needle.' Well, I am.

(Soundbite of sea gulls)

BOYCE: As we get close to land, he smokes a cigarette and watches the setting sun. Looking out at all the water stretching to the horizon, it's easy to imagine that the Alligator will stay lost for another 150 years. It's kind of crazy to search for such a small chunk of metal, almost as crazy as the 19th century inventors who dared to build submarines. Nell Boyce, NPR News.

INSKEEP: You can find blueprints of the USS Alligator and learn about its inventor by going to our Web site, npr.org.

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