NORTH CHARLESTON, S.C. — It could be one of the nation’s oldest cold case files: What happened to eight Confederate sailors aboard the H.L. Hunley after it became the first submarine in history to sink an enemy warship?

Their hand-cranked sub rammed a spar with black powder into the Union blockade ship Housatonic off Charleston on a chilly winter night in 1864 but never returned.

Its fate has been the subject of almost 150 years of conjecture and almost a decade of scientific research since the Hunley was raised back in 2000. But the submarine has been agonizingly slow surrendering her secrets.

“She was a mystery when she was built. She was a mystery as to how she looked and how she was constructed for many years and she is still a mystery as to why she didn’t come home,” said state Sen. Glenn McConnell, R-Charleston and chairman of the South Carolina Hunley Commission, which raised the sub and is charged with conserving and displaying it.

Scientists hope the next phase of the conservation, removing the hardened sediment coating the outside of the hull, will provide clues to the mystery.

McConnell, who watched the sub being raised more than eight years ago, thought at the time the mystery would be easily solved.

“We thought it would be very simple … something must have happened at the time of the attack,” he said. “We would just put those pieces together and know everything about it.”

But what seemed so clear then seems as murky now as the sandy bottom where the Hunley rested for 136 years. When the Hunley was raised, the design was different from what scientists expected and there were only eight, not nine, crewmen, as originally thought.

The first phase of work on the Hunley consisted of photographing and studying the outside of the hull. Then several iron hull plates were removed allowing scientists to enter the crew compartment to remove sediment, human remains and a cache of artifacts.

Thousands of people, many re-enactors in period dress, turned out in April 2004 when the crew was buried in what has been called the last Confederate funeral.

With the inside excavated, the outside of the hull will now be cleaned before the sub is put in a chemical bath to remove salts left by years on the ocean floor. The Hunley will eventually be displayed in a new museum in North Charleston.

Archaeologist Maria Jacobsen said the Hunley is like a crime scene except that, unlike on television shows, there is no smoking gun.

“If we compare this crime site investigation with, say, a tragic plane crash in the mountains, that investigation would be a lot easier,” she said. “You can go to the crash you can see the metal pieces and they have the fingerprints of the crash site.”

In the case of the Hunley, some of those fingerprints may be covered with the encrusted sediment on the hull that scientists refer to as concretion.

When the sub was found there was no window in the front conning tower, suggesting it had been shot out, perhaps by Union sharpshooters.

But no glass was found inside the sub and the remains of the captain, Lt. George Dixon, showed no injuries to his skull or body consistent with being shot while looking through the window, McConnell said.

The crew’s bodies were found at their duty stations, suggesting there was no emergency resulting in a scramble to get out of the sub. And the controls on the bilge pump were not set to pump water from the crew compartment, suggesting there was no water flooding in.

After the attack both Confederates on shore and Union ships reported seeing a blue light, believed to be the Hunley signaling it had completed its mission.

A lantern with a thick lens that would have shifted the light spectrum and appeared blue from a distance was found in the wreck.

But after the attack, the USS Canandaigua rushed to the aide of the Housatonic and there is speculation that the light could have come from that ship instead.

Could the Canandaigua have grazed the Hunley, disabling her so the sub couldn’t surface? A good look at the hull in the coming months may provide the answer.

Historians also know the Hunley needed to wait for the incoming tide to return to shore.

“Were they waiting down there and miscalculated their oxygen and blacked out?” said McConnell.

He said a grappling hook, believed to serve as an anchor of the Hunley, was found near the wreck. Cleaning the hull may produce evidence of a rope showing the sub was anchored, perhaps waiting for the tide to change.

Then there is the mystery of Dixon’s watch, which stopped at 8:23 p.m. Although times were far from uniform in the Civil War era, the Housatonic was attacked about 20 minutes later, according to federal time, McConnell said.

One theory is the concussion of the attack stopped the watch and knocked out the sailors on the sub. Or the watch simply might have run down and was not noticed in the excitement of the attack. That could have led to a miscalculation of the time they were under water.

Union troops reported seeing the Hunley approaching and the light through the tower window “like dinosaur eyes or a giant porpoise in the water,” McConnell said.

If the Hunley crew miscalculated and surfaced too close to the Housatonic on their final approach they would not have had enough time to replenish their oxygen before the attack, he said.

The clues now seem to indicate the crew died of anoxia, a lack of oxygen, and didn’t drown. “Whatever happened, happened unexpectedly, with no warning,” McConnell said.

Running out of oxygen can quickly cause unconsciousness.

“One you reach that critical stage, it’s like you flick a switch,” he said. “It’s that fast, like on an airplane.”