I can't attach the full 112 page document, but there was a fantastically insightful document into the possible causes of her loss. It analysed the evidence, witness testimony from other ships, the dynamics of the currents on Mioko Harbour and knowledge of how a submarine works, and concluded that she was probably lost to a Beam on Grounding.
Below is the relevant analysis:
6.6.3.9.2 Beam on Grounding
A beam on grounding, damaging Main Ballast Tanks and resulting in loss of stability, combining
with another event leading to a loss of buoyancy could lead to an uncontrolled descent to the
bottom with the pressure hull intact and crew secured or trapped inside the flooded submarine
seems the more credible of these scenarios. Given the lack of debris field or oil slick it seems
more likely that the submarine bottomed with the conning tower hatch secured and did not exceed
its crush depth. It remained disabled and intact on the bottom, either fully flooded through the
conning tower hatch or a breach in the pressure hull, or if the crew survived (judged unlikely),
unable to achieve sufficient buoyancy to surface.
6.6.3.9.3 Beam on Grounding Reconstruction of the Sequence of Events
A possible sequence of events may have been:-
x AE1 headed for Rabaul on the surface shortly after 1430, (say 1500) from the position
reported by PARRAMATTA.
x AE1 was under pressure to get back before dark and had about 30 minutes in hand to
make an ETA of 1750.
x The shortest route to the anchorage passed close by Mioko Harbour and the island of the
same name on the southern side of the Duke of York Island.
x AE1 had earlier deviated from the orders given for the day to patrol the southern
approaches to Rabaul, in order to check out a report on 13th September 1914 of a steamer
off the Duke of York Island - a final look through the entrance enroute Rabaul would have
been very tempting.
x Inexperienced in the local conditions, particularly the precautions necessary when
operating in proximity to coral reefs AE1 misjudged the strength of the current surging
NW towards the reefs and through the entrance to Mioko Harbour.
x As a result, AE1 found herself in a rapidly changing, dangerous situation, close in to the
reefs off the entrance, on a lee shore with the SE wind and strong NW current pushing
onto this hazard.
x Combined with the low height of eye and poor lighting to observe outlying reefs, defective
starboard shaft when running astern and the ever present possibility of a helm or
propulsion failure, AE1 was unwittingly standing into mortal danger.
x Looking up sun combined with the disturbed water arising from current hitting the near
vertical faces of the reefs (see Gus Mellon’s description of this at para 6.5.1.3 above) the
reefs were difficult/impossible to see.
x Whilst still making headway AE1 was washed beam onto a reef outcrop, opening up
numbers 1 and 3 main ballast tanks forward of the broadside tube on the starboard side.
x The force of the grounding was arrested by the athwartships bulkhead on the leading
edge of the broadside tubes annulus in the pressure hull (para 3.7.2 refers).
x The current held the submarine there, grinding and pivoting against the bulkhead with the
diesels still propelling ahead.
x The crew was thrown from their feet by the impact and working with a developing list took
several minutes to stop the diesels and to engage astern power on the port shaft. 81
This exacerbated the damage already experienced.
x With difficulty she extracted herself, using full power astern on the one (port) shaft
available and moved astern off the reef.
x The natural tendency of the port shaft running astern to pull the stern towards the reefs
(to starboard) was probably offset by the wind – most submarines have a strong tendency
to swing into wind when going astern.
x As a result AE1 moved off and in what direction it went is not certain but may depend on
where it grounded. A likely scenario is that it moved to the NE swinging to starboard, i.e.
making sternway away from the reefs and to the east, swinging to the south east, at the
same time, assisted by the NE running current also moving away from the harbour
entrance.
x In the process of moving clear it is possible that she struck a second time, adding to the
damage already experienced to her ballast tanks and pressure hull.
x A heavy list quickly developed as water flooded into the damaged ballast tanks, causing
difficulty for the crew trying to maintain their stations and regain control the submarine.
x A new factor or combination of factors then intervened, perhaps pressure hull was
breached at the broadside tube bulkhead leading to flooding and a loss of power as the
control room began to flood, with the starboard list channelling water towards the
switchboard and main batteries, perhaps the combined impact of astern power, rudder and
delicate state of stability combined to force the submarine onto her beam ends drawing the
conning tower hatch underwater, before the crew were able to close it, flooding the
submarine. We don’t know.
x As it sank it AE1 probably drifted further on the current before settling on the bottom.