The submarine H. L. Hunley conducted the first successful submarine attack on an enemy vessel, USS Housatonic, during the American Civil War but was lost with all hands because of unknown circumstances. The submarine has been recovered, and recent archeological findings have uncovered that a spar torpedo was used as opposed to a standoff torpedo that was commonly assumed to have been used. As a result, the submarine would have been in close proximity to the weapon when it exploded than previously thought. A multipart investigation has been conducted with the goal of determining if this reduced standoff distance could explain the mysterious loss of the vessel in the minutes or hours after the attack. Here, the results of a bottom-up naval architectural and weapons-effects analysis are reported. Together, the experimental, computational, and analytical results provide new insight to the vessel’s stability characteristics, propulsion, and dynamic loading environment during the attack. In addition, a discussion of possible loss scenarios, informed by both calculation results and inspections of vessel’s hull, is presented. Although the story of what happened to H. L. Hunley that night remains shrouded in mystery after this work, several important new research questions emerge.