Balancing myself on my hands, I drop into the hatch. My feet catch on a lip — the seat for another, inner hatch, perhaps. But it is missing, and so, camera in one hand, I carefully line myself up and drop into what I hope will be chest-high water. It turns out to be only waist deep. My feet hit sand, and I’m suddenly in darkness as my eyes adjust. I grab my camera and hit the flash, and see that I’m in an iron cavern that’s dripping with water and rust. I hit the flash again and look into the water. I wish I hadn’t. This submarine, half filled with sand, looks like a perfect haven for the region’s well known venomous sea snakes. At this moment, I know exactly how Indiana Jones felt in the Well of Souls. “Snakes. Why did it have to be snakes?” I jump up, catch the lip of the hatch and pull myself out of the hull just as my imagination pictures a tiny pair of fanged jaws reaching for my ankle. As I jump off the sub and wade to shore, I speculate about just what it is I’ve found on this deserted beach. Whose ancient submarine is it, and how did it end up here?

The truth is often stranger than fiction. A return trip to the beach in November 2002, this time armed with a tape measure and a pad for making notes, gives me more than a basic understanding of the submarine. I e-mail photographs of it around the world to colleagues who study old submarines. No one can figure it out, though one researcher, Gene Canfield, says it looks similar to Intelligent Whale, a submarine built for the Union Navy during the Civil War but never finished. Could it be that old? I wonder as I continue to send out my queries. Then, in mid-2003, I get an answer from Rich Wills, who thinks it looks more like another long-forgotten Civil War submarine, the Sub Marine Explorer. No one knows what happened to that sub, Rich explains. After the war, it ended up in Panama, working for the Pacific Pearl Company, harvesting pearls from deep-water oyster beds.

I sit up and take notice. After all, the wreck lies in the Bay of Panama, in an island group known as the Pearl Archipelago. But is it really a Civil War submarine that vanished from the pages of history after 1869? Could a submarine survive, half submerged on a tropical beach, for more than 130 years? Rich sends me a copy of a 1902 article on pioneer submarines of the nineteenth century. It reproduces a profile plan of Sub Marine Explorer and gives its basic dimensions. As I look at it, I smile. The profile matches perfectly, down to the placement and size of the conning tower. The rounded chamber at the top of the submarine with the forged iron braces would be filled with air for buoyancy. And, as I compare the measurements with my notes, it all fits. The 36-foot Sub Marine Explorer is a perfect match.

But how does Sub Marine Explorer fit into the history of submarine development? Built in 1865, what role did it play, if any, in the Civil War? And how does it compare with another recent discovery, the Confederate Civil War submarine H.I. Hunley? Found after years of hard work by Clive Cussler’s National Underwater and Marine Agency team and raised by the State of South Carolina, Hunley is one of the great archeological treasures of the Civil War, on a par with the ironclad USS Monitor, whose engine and turret have also been pulled from the depths. Even as I sit pondering the mysteries of Sub Marine Explorer, a team of archeologists is carefully excavating and dismantling Hunley to reveal its secrets. So for the answers on Sub Marine Explorer, I turn to Hunley project historian Mark Ragan. “There’s no one better,” Clive tells me as he reads Ragan’s number to me over the phone.

Mark answers his phone with a laconic drawl that quickens with excitement as I tell him what I’ve found on a Panamanian beach. I e-mail him a handful of photos, and as he opens them on his computer 3,000 miles away, I hear the subtle but sharp intake of his breath. That’s a good thing, because Clive is right. No one knows Civil War submarines better than Mark Ragan. He literally wrote the book on them, and he now turns his considerable energy and skill to dig deep into the archives to learn more about Sub Marine Explorer and its inventor, a forgotten American engineering genius named Julius H. Kroehl.

War spurs terrible and magnificent inventions, often taking ideas and concepts developed in peacetime and testing them hurriedly in times of crisis. During the Civil War, technology played a significant role. Among other innovations, the war introduced new guns and more powerful cannon, ironclad warships with rotating turrets, undersea mines — and the submarine. There was nothing new about each of these inventions save their first practical and deadly use in combat. The pioneering naval accomplishments of the war started with the attack on the wooden fleet of the Union Navy at Hampton Roads, Virginia, by the Confederate ironclad CSS Virginia, demonstrating that this new type of warship doomed the “wooden walls” that had dominated naval warfare for centuries. The first clash between ironclads took place when the Union’s USS Monitor interceded between Virginia and the Union wooden fleet the following day and fought the Confederate ship to a standstill.

Another innovation was the use of an electrically detonated “torpedo,” or mine, one of which sent the Union’s ironclad Cairo to the bottom of the Yazoo River, giving the ill-fated gunboat the dubious distinction of being the first warship in history to be sunk by a mine. Later, there was the brave but doomed sortie of the Confederate submarine H.I. Hunley into Charleston Harbor to sink the Union warship Housatonic with a spar-mounted “torpedo” projecting from her bow. Shortly after this victory, Hunley sank, taking her crew with her, just a few hundred yards from her victim. No one knows why Hunley sank, but the tiny craft gained fame as the first submarine to destroy an enemy vessel in combat. Quickly buried by silt, Hunley’’s grave remained undiscovered for 150 years.

As for submarines, both sides embraced this new technology. Inventors proposed various underwater craft and built some that operated with various levels of success, killing their builders and crews on more than one occasion. A number of projects were launched, some in secrecy, others more publicly, leaving behind an unfortunately incomplete record of pioneer submarines and submariners. But the rediscovery of Julius Kroehl’s Sub Marine Explorer and a slow unraveling of his wartime career, buried in the National Archives, suggests that at every step of the way, as the Confederates developed both their “torpedoes” and submarines, Kroehl was there to develop something to counter them for the Union side. It may well be one of the last great untold stories of the Civil War.

Julius Kroehl was a German-born immigrant who came to America in 1838. He studied to become an engineer, and in 1845 he won a U.S patent for a flange-bending machine for ironwork. In 1856, he was well enough established to win a contract from New York City to build a cast-iron “fire watch tower” in Manhattan’s Mount Morris (now Marcus Garvey) Park. In an age before fire alarm boxes, volunteer fire fighters watched the city from towers, ringing a bell to sound the alarm.

But Kroehl’s real interests lay underwater. At the same time that he was engaged in his fire tower project, Kroehl and his business partner, Peter Husted, were contracted by the City of New York to remove part of Diamond Reef, near Governor’s Island in the East River, as it was a hazard to navigation. According to the Scientific American of August 5, 1856, “Messrs. Husted & Kroehl” were blasting to remove 6 feet of depth on the 300-foot reef. “Large tin canisters attached to the lower ends of strong pointed stakes, are sunk to rest on the face of the reef, and are discharged with a galvanic battery.” It was on this job that Kroehl became interested in diving. In 1858, Husted and Kroehl hired a new partner, Van Buren Ryerson, who had just built a pressurized diving bell that he called Submarine Explorer. Eight years later, Kroehl used the basic principle of Ryerson’s bell to build the world’s most sophisticated submarine.