The article says the HUNLEY’s spar explosive detonated the gunpowder and other explosive aboard the USS HOUSATONIC, resulting in an explosion perhaps one hundred times stronger than the HUNLEY’s crew had expected. The much larger than expected explosion of the USS HOUSATONIC they speculate immediately killed and/or rendered the crew of the HUNLEY unconscious with its tremendous concussion wave passing through the sea to strike the nearby HUNLEY and its crew. The HUNLEY it is believed then drifted for a distance with its dead and/or unconscious crew before flooding and sinking to the seafloor.
Isn't it interesting? The article also says:
"Some historians say that the submarine showed a mission-accomplished lantern signal from its hatch to troops back on shore before it disappeared. Soon after the signal had been fired, the sub sank about 4 miles (6.4 kilometers) off Charleston."