SAN FRANCISCO — For nearly a century, the disappearance of the USS Conestoga, with 56 officers and sailors on board, remained one of the U.S. Navy’s great maritime mysteries.

But over the past year and a half, intrepid research, days on the high seas and haunting photographs helped finally solve the sensational saga, which grabbed national headlines in 1921 and spurred a search as immense as the one for Amelia Earhart’s plane a decade later.

On Wednesday, scientists with the National Oceanic and Atmospheric Administration, including one with San Jose roots, announced the discovery of the naval tugboat near the Farallon Islands — some 2,000 miles from where the searches had centered near Hawaii and Mexico 95 years ago.

“I’m a maritime archaeologist. I’ve worked around the world. Name seven seas, and I’ve been there, but not every wreck you work on has the kind of importance as the Conestoga,” said Jim Delgado, director of NOAA’s Office of National Marine Sanctuaries’ Maritime Heritage Program, who spent his teen years rescuing Native American remains from construction sites in South San Jose in the 1970s. “With the Conestoga, this is the first time in my career I’ve been privileged to work on something that we’ve been able to bring closure to families.”

Although Delgado and his team confirmed their discovery in October, they waited until they had tracked down as many relatives of the crew as they could find before making the formal announcement Wednesday in Washington, D.C.

One of those family members was 67-year-old Peter Hess, of Marin County, who was often told growing up that he resembled his cousin one generation older, Chief Petty Officer George Kaler, who left his small farming town in Ohio to join the Navy.

“How ironic,” Hess said. “I used to cross the Golden Gate for four decades and always looked to the right to see if I could see the Farallon Islands, and that’s the final resting place of the Conestoga?”

The tugboat left Mare Island Naval Shipyard in Vallejo on March 25, 1921, setting course for Pearl Harbor, then American Samoa, where it would work as a station ship. Crew members wrote in letters home that they were “heading to paradise” and the captain’s wife and 3-year-old daughter were making plans to join him there.

Instead, Conestoga vanished, and conflicting reports and sightings resulted in 60 planes and destroyers looking near Hawaii. A drifting lifeboat with the letter “C” later sent teams to Baja, Mexico.

A clue headlined in the Mercury Herald in May of that year that a Conestoga life vest was found at Moss Beach, near Pacific Grove, was ignored.

In fact, the Conestoga didn’t make it 24 miles beyond San Francisco — it sank within 24 hours in a storm just 3 miles from Southeast Farallon Island.

It wasn’t until 2014, however, when NOAA decided to investigate a sonar target detected in 2009 as part of a survey of shipwrecks off the coast of San Francisco and the Farallones. At the time, Delgado and Robert Schwemmer, NOAA’s West Coast regional maritime heritage coordinator, hadn’t even heard of the USS Conestoga. They dropped the remotely operated vehicle, or ROV, into the water and “what appeared out of the gloom was the bow of a ship,” Delgado said.

He recognized it as a tug, complete with its riveted steel hull, steam steering apparatus, marine steam engine and big winch for towing. It was extra long at 170 feet.

“As we looked, one thing became very clear,” Delgado said. “This isn’t something that had been used to the end of its life and was scuttled. Everything suggested this is a ship that had fought and had died in service, but what ship it was we didn’t know.”

Schwemmer’s research found a list of 400 wrecks in the area, “but no wreck showed up in the books that matched what we were seeing.”

The wreck was covered with vegetation and sea life, so no name clearly emerged through the murky waters. The scientists took the images back east and studied them.

“In detective stories, you always look for the smoking gun,” Delgado said. “Well, sitting inside the hold as though it had fallen forward was a 3-inch 50-caliber, a single purpose gun. Civilian tugs don’t carry guns.”

That’s when they focused their attention on naval vessels and stumbled on the mystery of the USS Conestoga. They pored through hundreds of documents and came upon a photo album of the ship and crew, taken by a professional photographer on the ship’s previous stop, in San Diego. To the scientists, the images of the white-hatted sailors were mesmerizing and compelled them to move forward.

“I saw their eyes. I saw their picture. I saw that they were proud,” Schwemmer said in an interview Wednesday. “We just needed to make things right for them.”

One of the photographs provided the clue that unlocked the mystery. Schwemmer called Delgado and said, “Look at this.”

A half-dozen sailors stood on deck, smiling at the camera. They stood next to a 3-inch, 50-caliber gun.

“For the two of us and the rest of the team, when you look at that and see them there staring back at you across time, you get it,” Delgado said. “It’s all about the people.”

He had a similar feeling when he found the remains of a Native American woman on a construction site off Bernal Road in South San Jose in the early 1970s. She wore a shell necklace, and he knew that she was loved. Delgado, with help from former Mayor Norm Mineta, returned those bones to the local Ohlone Indians for reburial.

Finding the photographs of the sailors compelled him to find as many families as he could — about 30, with the help of a genealogist. He’s hoping to find more.

“This not only helps bring closure, but it sends out another message to these guys that if you serve and if you paid the price for that service, you should not be forgotten,” Delgado said.

In October, the NOAA team went out to the wreck again, this time taking Hess with them. Without any word on what happened to their cousin, Hess’ family liked to believe he was living out his days on a Samoan island, dancing in a grass skirt.

Now, they can say goodbye.

With Navy admirals joining them on board, Hess and the NOAA team held a solemn service for the 56 souls lost at sea, where the USS Conestoga will remain undisturbed. Together, they scattered white rose petals on the sea until the flowers formed a wreath around the wreck below.

Contact Julia Prodis Sulek at 408-278-3409. Follow her at Twitter.com/juliasulek.