Karl Stanley's homemade submarine has sprung a leak. It's a discovery both fortuitous and disconcerting. Fortuitous because I notice it as we bob on the surface of the placid Caribbean Sea, just a few hundred feet off the Honduran island of Roatán. Disconcerting because it's 8:30 p.m. and we're about to spend the night 1,600 feet down searching for the six-gill shark, an enigmatic 15-foot, 1,300-pound predator that patrols these depths.

"That's just the O-ring," Stanley reassures me as water wells up in the window and drips to the floor. Apparently the rubber washer meant to seal the window separating us from watery doom is feeling a touch rebellious. "It doesn't have enough compression on it. Hopefully it will fix itself under pressure." Stanley is a problem solver, and he casually throws me a towel to wipe up the moisture, more concerned about the corrosive properties of saltwater than the possibility of a catastrophic breach.

The words homemade and submarine aren't commonly paired, but Stanley, a 34-year-old self-taught engineer, has built two DIY subs, safely logging more than 1,000 dives. Still, sitting in Idabel, the cramped three-person craft he built on a shoestring, I can't help but recall that a faulty O-ring caused the space shuttle Challenger, with its NASA Ph.D.'s and multi-billion-dollar budget, to blow up. Stanley turns a handle, filling the ballast tanks with water, and we begin to sink into unexplored darkness.

Our slow descent accelerates into free fall, and bioluminescent plankton bounce off the submarine, exploding in a blizzard of light. At 100 feet the leak seals, as Stanley predicted, and I feel better about the prospect of finding one of the sharks, which we hope will be attracted by our gruesome hood ornament, a pig's head tied to the front of the submarine.

We plummet through the photic zone, the fertile band of water shallow enough for the sun's rays to power photosynthesis. To my right sits a very squished Martyna Mierzejewska, a 30-year-old Polish-Canadian dive instructor who plunked down $500 for the privilege of role-playing a canned sardine. Stanley, tall and thin like the coconut trees that line the beach near his home, on Roatán's Half Moon Bay, stands in the turret of the L-shaped submarine, driving; he's been taking paying customers down in his homemade subs for a decade. At 660 feet, we leave the photic zone, crossing the ocean's Mason-Dixon line toward the deep sea, the largest ecosystem on the planet, where life is shackled by a dearth of sunlight. Stanley celebrates crossing the invisible boundary with a game of interspecies Morse code, flashing the sub's lights to stimulate the glowing plankton, which respond by burning brighter.

At 1,600 feet, the deep sea's processes complement one another nicely, acting as both trash compactor and refrigerator. More than 700 pounds per square inch—nearly 50 times the pressure at sea level—squeezes the little yellow submarine, and the water temperature has dropped from the low eighties to the low forties. This is the netherworld that Stanley affectionately refers to as "my zone."

"If you add up the man-hours spent between one and two thousand feet," he boasts, with equal parts honesty and self-aggrandizement, "I'm dominating that category. If I haven't been there before, no one in the history of humankind ever has."

Stanley is an explorer, not a diplomat, and the audacity that serves him so well in the deep can alienate others on land. "Karl has a very scientific mind," says his friend Jeff Thekan, 55, who sells real estate on Roatán. "He only sees things in black and white. There's no gray, and that can get him into trouble." Stanley is feuding with his neighbor on the island, and the vice mayor wants him deported. After nine years on Roatán, his position has become so precarious that he spent a week in Dominica last November scouting a move. "He's pissed off the wrong people," says another friend, 25-year-old American expat Kristen Davis. "I wouldn't say he is well liked around here, but few pioneers are."

Meanwhile life at 1,600 feet continues untouched by politics, and we proceed with our shark hunt. Six-gills have weak jaws, which requires them to tear off their prey's flesh by thrashing around. Stanley knows the technique well—six-gills have spun his submarine 180 degrees while violently ripping off pork chunks. He has seen them dozens of times, and they generally take anywhere from 30 minutes to five hours to appear, so we wait. And wait. And wait.

Submarines are not roomy vehicles. With no bathroom on board save emergency sanitary bags, a sub dive is an exercise in bladder control. Tourists typically spend three and a half hours in the sub, but Stanley has repeatedly overnighted at depth. Idabel carries enough life support and air-cleaning carbon-dioxide scrubbers to keep us alive for three days, but without an abyss-to-surface communication system, it's improbable we'll ever be found if we run into trouble.

For eight hours we smush together, a tangle of knees and elbows and hip bones, a claustrophobe's nightmare. Finally, at 5 a.m., Stanley says, "We can't stay down here forever." As we head for the surface, I ask him why our normally curious quarry was so elusive. He thinks it might be the two-day-old pig's head. "It's so coagulated that it has stopped bleeding, but it isn't old enough to really stink yet," he says. He pauses, then offers a submission to the Understatement of the Year contest. "I mean, this isn't an exact science."