In August 2017, Rachel Lance published a third paper presenting her finding that the torpedo explosion likely caused soft tissue injuries that instantly killed the crew.  See this Duke University article that includes a video of Lance describing her analysis.  It is important to understand that this study, which analyzed the probability of soft tissue injuries to the lung and brain, does not contradict but rather complements the Naval History and Heritage Command analysis, which used models to evaluate the likelihood of skeletal injuries.  Still the paper generated a strong negative response from the Friends of the Hunley, possibly because the Duke-generated stories stated flatly that the mystery was solved, although the paper itself gives a 16% chance the crew survived.  The Naval History and Heritage Command has also spoken up, apparently conflating the skeletal and soft-tissue analyses.  All of this may actually be good news, leading to much more academic attention to publishing research about the Hunley.

In my opinion, the accumulation of evidence more and more supports Kim Johnson's theory, presented below, that the crew were killed or severely incapacitated during the attack.

The remaining mystery is how the the Hunley ended up 1000 feet from the site of the attack.  The inlet pipe is sheared where it joins the flange that attaches it to the hull.  The break is consistent with flexing of the hull plate relative to the attached pipe.  The current opening is so large that the sub would have filled so rapidly that it would have sunk to the bottom much closer to the Housatonic.  So either the leak was somehow slowed, a difficult operation because of the nature of the break, or the pipe, though broken, immediately displaced only a small amount.  You can see in this simplified site plane drawing that the Hunley was 

found lying atop its rudder, indicating that it hit the bottom hard, stern first, breaking off and riding over the rudder, or sometime later, the wreck was moved violently sternward, breaking the rudder off at that time.  In either case, I propose that it was this event that displaced the broken pipe to its present dislocation.  In this scenario the original offset could have been small enough to allow the Hunley to drift all the way to its resting place. 

 

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It's interesting that the response to the soft-tissue study brings up all the loss theories again, as if there is no new evidence to support or refute them.  Here's an evaluation of the 2007 theory bullet list discussed below, with supporting or contradicting evidence (grayed-out bullets are less or unlikely, again in my opinion):

• A bullet form the Housatonic ... - Did the crew of the submarine H.L. Hunley suffocate?, Lance, 2017 indicates that the damage from a bullet is not consistent with the final location of the Hunley. 
• ... damaged during the torpedo explosion ... - Science Meets History: Incident Analysis of H. L. Hunley, Naval History and Heritage Command, 2017 indicates observed damage to Hunley is consistent with torpedo explosion effects, but the broken ballast tank inlet pipe is not consistent, as is, with the final location of the Hunley. 
• ... fatal collision ... - Does Erosion Corrosion Account for Intriguing Damage to the Hull of the Civil War Submarine H.L. Hunley?, Jacobsen, 2012 indicates that damage to hull did not happen on the night of the attack.
• Dixon took the sub to the bottom ... Did the crew of the submarine H.L. Hunley suffocate?,  Lance 2016  indicates that carbon-dioxide poisoning would occur before oxygen starvation and is inconsistent with the positions of the crew [In full disclosure, I'm listed a co-author of the paper, although I provided only technical data on the submarine; I was not involved in the hypoxia/hypercapnia analysis]; Air blast injuries killed the crew of the submarine H.L. Hunley, Lance, 2017 concludes the crew was likely killed by the torpedo explosion.
• Dixon scuttled the damaged Hunley - Ibid.
• The crew succumbed to loss of oxygen ... - Ibid. (It's important to note that the Payne Stewart accident was due to a loss of oxygen and not a buildup of carbon dioxide.  Lance's 2016 suffocation paper describes the distinct effect of each.)
• ... similar fate while waiting ... - Ibid.
• A sudden storm ... - See Union Court of Inquiry regarding reported weather.

The following overview, dating up to 2007, is not comprehensive, but presents a historical overview of pertinent information and speculation prior to publication of the papers cited above.  Some of the material is still pertinent. 

The April 2006 Blue Light summarized some of the theories and offered some thinking from the Friends of the Hunley.  The lay expert members of the Yahoo Hunley group have discussed various theories in depth and George Penington has provided a forum in his newsletters.  Some of us hold passionate views on the subject, but all are based on evidence.  At the risk of leaving something out, here is a list of possibilities, in no particular order:

• A bullet from the Housatonic broke one of the view ports, causing a fatal leak and possibly injury to George Dixon.
• The Hunley was damaged during the torpedo explosion, resulting in leaks, loss of control, and or injury to the crew.  In one scenario, presented in detail by Kim Johnson, the Hunley descended stern-first to the bottom immediately after the explosion.
• The Hunley suffered a fatal collision with the Canandaigua, on its way to aid the sunken Housatonic, or was swamped during a near miss.
• Dixon took the sub to the bottom to wait for the tide to change or to wait out the heavy Union ship activity in the area and was unable return to the surface.
• Dixon scuttled the damaged Hunley to prevent the submarine from falling into Union hands.
• The crew succumbed to loss of oxygen or to carbon dioxide poisoning as they cranked toward the shore, and the sub drove to the bottom - the so-called "Payne Stewart" scenario.
• The crew suffered a similar fate while waiting on the bottom.
• A sudden storm arose and swamped the Hunley.

• The submarine has three areas of obvious damage and other perhaps less obvious signs:  

• A large hole in the forward hatch tower just above the port-side forward view port,
• A small hole in the forward ballast tank on the starboard side, and
• A very large hole in the aft tank on the starboard side.
• The propeller guard upper forward starboard side has a number of large jagged gashes.  (The port side is missing.)
• The rudder is detached and was found under the hull.
• The starboard dive plane is set at a different angle from the port plane.

• Forensic reports on the crew reveal no recent or fresh injuries.
• A Confederate report mentions receipt of a pre-arranged signal from the Hunley, after the attack.
• A lantern, probably capable of signaling, was found on board.
• An independent Union report mentions a light on the water in the vicinity of the Housatonic .
• The Hunley's forward hatch was not latched and is currently slightly ajar.  
• The crew were found more or less at their stations, although the remains of the last two crewmen and those of two just aft of Dixon were more commingled.
• The submarine made virtually no progress back to shore from the attack site.
• According to Conlin and Russell (Nautical Archaeology – “Archaeology of a Naval Battlefield: H. L. Hunley and USS Housatonic”, Apr 2006) the Hunley was found 900 feet east of the stern of the Housatonic .  (Note that many other values, down to 650 feet, have been given for this distance over the past several years.)
• Analysis of the sediment within the Hunley indicates, because the lowest layers are very fine, and only the uppermost contain coarse material, there was no large breach in the hull until a considerable amount of fine material seeped in.
• The same sedimentary evidence indicates the cabin filled from the front. 
• There are stalactites in the concretion within the cabin.  This point deserves comment here.  It was reported early in the excavation that this was evidence of a dry cabin.  Bruce Kinsey recounted a conversation he had with conservator Paul Mardikian in which Paul stated these were a kind of phenomenon that could not occur under water.  If this is true, a good part of the cabin remained dry for a long time.  In Secrets of a Civil War Submarine, however, Sally Walker relays geologist Scott Harris's statement that submerged growth of these features is possible.  In 2007 Bruce Kinsey reported conversations with the scientists indicating their current belief that these features most likely formed under water.
• The Union Court of Inquiry into the Housatonic's sinking provides information on the weather.  Various witnesses report good weather, smooth seas, and light to moderate wind.  The tide was half-ebb.
• The night was clear with a three-quarter moon.

     The Blue Light article recounts another historical report that I think might account for some of the observed damage to the Hunley.  First let me digress to a some pertinent archaeological evidence.  An earlier Blue Light included a site drawing by James Hunter of the Hunley on the bottom.  I've reproduced a schematic version of the drawing here:

What does this tell us? 
These are not the only possibilities but at the moment I think they are more likely than some others.

• If Dixon gave the blue light signal, the submarine survived the initial attack but may have had damage, perhaps disabling damage such as a non-functioning rudder.  (Of course it is possible he gave no signal and the sub survived, but we're only extrapolating evidence here not covering every possibility.)
• If he didn't give the signal, the Hunley may have gone down immediately but certainly moved some distance from the Housatonic.  Since the sea is only about 30 feet deep in the area, the submarine traveled much farther laterally than down.
• In either case the damage to the hull was not catastrophic, that is, there was no large hull breach.  This does not rule out a steady leak or leaks. 
• There was considerable Union activity that night after the Housatonic went down and at best Dixon would have to navigate through relatively crowded waters.  The Fleming report, if actually Dixon's signal, put the Hunley close to the Canandaigua.  The possibility of an accidental fatal encounter with the Union ship is not far-fetched.
• The night and seas were calm and the tide was turning in Dixon's favor.  He may have had the choice of starting for the shore, perhaps submerged to avoid detection, or of waiting for the tide to assist his tired crew in coming home.  If he took the second choice he may have also decided it was safer to wait submerged.

So consider the two choices and conceivable outcomes.

• Dixon makes for shore.  His crew is tired but excited by their successful attack.  He believes the longer he stays in the area, the more likely the sub will be discovered.  Perhaps, when he opens the hatch to give the agreed signal he sees the Canandaigua coming his direction and elects to make the run submerged after getting a bearing.  The crew passes out from lack of oxygen or too much carbon dioxide during the trip home and the submarine settles to the bottom.
• Dixon assesses his crew and decides his best choice is to give them a short rest and wait for the assist of the tide to get home.  He takes advantage of the submarine's ability to wait on the bottom.  The crew falls asleep or passes out while waiting and succumbs from lack of good air.  Perhaps, as Dan Dowdey suggests, the sub becomes mired in the bottom sediment and couldn't be raised.

Either of these scenarios could have been complicated by leaks in the hull that necessitated some of the crew operate the pumps.  Such activity would slow progress in the first case and used more air in the second.

But perhaps this sort of bottom-up analysis, looking at facts and trying to interpret what they tell us, is the wrong approach for solving the problem.  Perhaps we should  take a more top-down approach and look at a basic, incontrovertible fact and ask what it tells us.  The Hunley made virtually no progress toward home after the attack.  Why would this be?  The following possibilities suggest themselves immediately:

• The Hunley went down almost immediately.  Similarly, the crew was incapacitated and the submarine drifted and sank.
• The Hunley was damaged and could make no progress home.
• Dixon saw all the activity in the area and decided to wait, maybe on the bottom, for the tide to make his passage quicker, or for the activity to slow down.

A little thought suggests a few other, perhaps less likely possibilities:

• Dixon misread his heading and started off in a very wrong direction, discovered his error and started back.
• Dixon headed off in another direction to avoid the Union ships and so made little net progress before disaster struck.

We can evaluate these possibilities by examining each of the facts and possible facts listed earlier to see how they fit, and wait for new information as it is discovered and revealed by the scientists working on the submarine.

The Yahoo Hunley discussion group, previously linked here, is unfortunately gone.