Unfortunately, the Hunley and her crew of nine including her commander Lieutenant Dixon, never returned. While comrades and loved ones watched anxiously the next morning, her mooring continued to remain empty. Finally it was presumed that she, too, was lost in the explosion of her own torpedo.

After extensive and exhaustive research it is now been proven that the Hunley did not go down with the Housatonic. In fact, the men of the Hunley had successfully accomplished their mission and were on their way back when some unknown tragedy struck. By prior agreement, the Hunley had arranged for a signal to be displayed from shore after they had completed their attack to help guide them on their return. Dixon and Lt. Colonel O.M. Dantzer, commander of Battery Marshall, had settled on two blue lights to be shown from the Hunley and a single white light to be displayed from shore. A full one-half hour after the attack, a Federal sailor, Robert Flemming, who was in the rigging awaiting rescue, testified that he saw a blue calcium light off the starboard quarter. Colonel Dantzer, in his official report, confirms that the blue lights were observed and answered from his station on shore.

The little Hunley and her crew, therefore, were on their way in. What elation they must have felt! With their new weapon, they had attacked and sunk one of the largest warships in the U.S. Navy. All their training and perserverance had finally paid off. Then, at some point, tragedy struck. Perhaps one of the glass portholes had been hit by rifle fire and finally gave way. Possibly, while showing the blue lights, a swell swept over them and with the hatches open the interior flooded. Like other great undersea craft of a later century, the Hunley just simply disappeared.

All of this speculation and previous reports have now become meaningless. By plotting a course between the wreck site and the point where the Hunley departed that cold February night, researchers in 1994, using high tech electronic gear, uncovered two large metal anomalies buried deep beneath the mud and sand. It was believed that one of these anomalies represented the hull of the Hunley. Finally, on May 3, 1995, these same researchers, led by well-known author Clive Cussler, who has devoted fifteen years to the search, successfully uncovered one of the Hunley's hatches. With this positive identification it was determined that the encrusted iron hull is intact and lies buried on her side in twenty feet of water, and only a couple of miles off shore.