That could settle a long-standing argument among historians.
The loch was also the site of a 1944 disaster in which six tank landing ships preparing for the secret invasion of Saipan were destroyed in an ammunition explosion that killed 200 sailors and wounded hundreds more.
When the Navy scooped up the remains of the so-called LSTs and dumped them outside the harbor to protect the secrecy of the invasion, it apparently also dumped the mini-sub's remains, which were mingled with the damaged U.S. ships.
"It's not often that a historian gets a chance to rewrite history," said marine historian and former Navy submariner Parks Stephenson, who pieced together the evidence for the television program "Nova." "The capsizing of the Oklahoma is the second most iconic event of the attack. If one submarine could get in in 1941 and hit a battleship, who knows what a midget sub could do today. Iran and North Korea are both building them. It's very worrying."
Stephenson and his colleagues have put together a convincing chain of circumstantial evidence, but it is just circumstantial, said Burl Burlingame, a journalist at the Honolulu Star-Bulletin and author of "Advance Force: Pearl Harbor."
"There is a good chance that this is the Pearl Harbor midget, but I don't think the case is closed on it," Burlingame said. "At this point, it is not hard evidence."
The two-man, 80-foot-long sub in question does not have a name of its own. Each of the five subs in the attack was carried by a conventional submarine and took its name from the mother boat. It is thus called the I-16-tou -- tou being Japanese for boat. Powered by a 600-horsepower electric motor, the sub could reach underwater speeds of 19 knots, twice as fast as many of the U.S. subs of the day.
The three pieces of the sub were found during routine test dives between 1994 and 2001 by Terry Kerby, chief pilot of the Hawaii Undersea Research Laboratory's submersibles Pisces IV and Pisces V. But Kerby and others assumed they were a part of a war trophy that had been captured by allied forces at Guadalcanal or elsewhere, towed back to Hawaii and scuttled.
Stephenson got involved in 2007 because he was looking for the fifth Japanese mini-sub.
In 1941, a crewman on the I-16 had received a radio call from the I-16-tou at 10:41 p.m. on Dec. 8 reporting the success of its mission. That indicated to Stephenson that the mini-sub had found a calm place in the harbor and hidden until the next night before surfacing and sending the call.
The crew members would have then scuttled the craft because they could not get it out of the harbor. The West Loch would have been a good location to hide, but researchers could find no trace of the boat there.
A diver who had been looking for the mini-sub suggested that Stephenson talk to Kerby, who sent him pictures of his find.
"As soon as I saw the bow section with the distinctive net cutter, I knew that we had found the fifth midget sub," Stephenson said. The Japanese navy modified net cutters on the subs for specific missions, and the one on the wreck was identical to those on the other mini-subs.
No torpedoes were found on the wreck, and evidence suggests that they were not present when the boat was sunk. A newly declassified photograph taken by a Japanese plane during the attack appeared to show a mini-sub firing a torpedo into Battleship Row. A report to Congress in 1942 by Adm. Chester W. Nimitz describes an unexploded 800-pound torpedo recovered after the battle. That's twice the size carried by the torpedo bombers.
That torpedo was apparently a dud that missed the West Virginia.
But an examination of the remains of the Oklahoma shows that it apparently had underwater damage much larger than that associated with aerial torpedoes. An underwater blast would have caused it to capsize, Stephenson said. "Otherwise it would have settled to the bottom upright," like the other sunken ships.
The 1944 disaster at West Loch occurred on May 21 as the Navy was preparing to invade the Mariana Islands in Operation Forager. The Navy clamped a top-secret classification on the incident to keep it from the Japanese, and few records are now available. What is known is that it was crucial to clear out the debris because the loch was by then the site of an ammunition dump.
Records from the salvage ship Valve showed that it was brought into the loch during the cleanup and its 250-ton crane was used for an undisclosed reason. Stephenson thinks it lifted the I-16-tou, but there are no records to confirm that.
The remains of the mini-sub were then dumped three miles south of Pearl Harbor along with those of the LSTs, to be found by Kerby 50 years later.
Bulkheads on the wreck are sealed, so researchers don't know whether the mini-sub crew was trapped. But a map taken from one of the other mini-subs showed the location of a safe house in Pearl City, Hawaii, suggesting the crew might have scuttled the boat and escaped.
The "Nova" episode describing the search for the I-16-tou will air Jan. 5.