The disappearance of the Conestoga on March 25, 1921, had been considered one of the Navy's greatest unsolved mysteries.
Until now, that is.
Researchers say they've found the wreck near the Farallon Islands, just 30 miles off San Francisco.
The wreck was first spotted in 2009 during a National Oceanic and Atmospheric Administration (NOAA) hydrographic survey near the Farallon Islands.
At the time it was listed as a "probable, uncharted shipwreck."
Working with the Navy, NOAA was able to confirm in October that they had found the remains of the Conestoga.
"Thanks to modern science and to cooperation between agencies, the fate of Conestoga is no longer a mystery," Assistant Secretary of the Navy for Energy, Installations and Environment, Dennis V. McGinn, said in a Wednesday news release. "In remembering the loss of the Conestoga, we pay tribute to her crew and their families, and remember that, even in peacetime, the sea is an unforgiving environment."
Cameras on remotely-operated vehicles captured images of the wreck:
In the initial confusion after the Conestoga vanished, the ship was first incorrectly reported as having safely arrived at Pearl Harbor.
The search for the ship didn't begin until more than five weeks after it left San Francisco -- and even then, it was concentrated in the wrong area, focusing on waters near Pearl Harbor, some 2,000 miles away.
The only trace of the ship ever found came nearly two months after the disappearance, when a lifeboat with the letter "C" on its bow turned up near the coast of Mexico.
The ship was officially declared "lost" on June 30, 1921, more than 3 months after it set sail.
It was also the last U.S. Navy ship to go missing in peacetime.
"After nearly a century of ambiguity and a profound sense of loss, the Conestoga's disappearance no longer is a mystery," Manson Brown, assistant secretary of commerce for environmental observation and prediction and deputy NOAA administrator, said in the news release.
The agency also issued an archaeological report on Wednesday that reveals what may have sunk the ship and doomed its crew. The report states:
"The seas were rough, with high waves. Based on the position of the wreck and the weather report, we believe Conestoga ran into trouble outside the San Francisco Bar soon after leaving the Golden Gate. Heavy seas past the Farallones may have caused the tow, allegedly a barge, to break free. Careful examination of the tow winch on the wreck shows the wire is twisted and not neatly spooled on the drum, which suggests a towing problem."
The report says, however, that towing the barge didn't cause the ship to sink. It was the condition of the ship itself -- known as a "wet vessel" because it was prone to taking on water -- combined with bad weather.
It had problems with the bilge pumps and went steaming into gale-force winds on that cold March night.
"Within a matter of hours, if she was towing a barge it was lost, and the tug was taking on too much water to remain afloat," the report states.
The crew then headed for the only place they would have a chance at any kind of refuge: Southeast Farallon Island.
"This would have been a desperate act, as the approach is difficult and the area was the setting for five shipwrecks between 1858 and 1907," the report states. "However, as Conestoga was in trouble and filling with water, it seemingly was the only choice to make."
They never reached the island.
"Ultimately, the incoming water overtook them, despite their professionalism, attention to duty and hard work, and Conestoga sank, with a loss of every man on board," the report concludes.
Images from the remote dives show that while the wood deck has collapsed due to age and corrosion, much of the rest of the ship is largely intact.
The cameras spotted some of the Conestoga's distinctive features, including its propellor, steam engine and boilers, and the 3-inch, 50-caliber gun that had been mounted on the main deck.
The cameras also picked up white plume anemones, wolf eels, ling cod and rockfish.
No sign of human remains were spotted, but the ship is considered a military grave for the 56 who lost their lives.
The site of the wreck is protected by the Sunken Military Craft Act, which protects "sunken military craft that are owned by the United States government, as well as foreign sunken military craft that lie within U.S. waters."