Roman Totenberg, left, performs with composer Samuel Barber. (Family photo via National Public Radio)

The master violinist, who had fled his native Poland and played in the greatest halls of the world, pegged the suspect from the start. Philip Johnson.

That Thursday night in 1980, Roman Totenberg had been momentarily distracted, mingling at a reception after a concert in Cambridge, Mass. He remembered Johnson, a player in his 20s, milling about. And after the terrible theft — of a 246-year-old Stradivarius, out of his office at the Longy School of Music — the younger man’s ex-girlfriend even came to Totenberg. She also suspected Johnson.

These suspicions did not move the police, who refused to file for a search warrant. But on Thursday in New York, Totenberg’s hunch proved right. Three years after the violinist’s death, the U.S. attorney’s office turned over the Stradivarius, now 281 years old and worth millions, to his three daughters, one of whom is Nina Totenberg of National Public Radio.

“I never knew that he had it,” said Thanh Tran, Johnson’s ex-wife, whose discovery of the violin earlier this summer led to its fast return. “I was flabbergasted when I found out. I think maybe he was afraid to give it back. How can you just steal something like that and give it back? It’s a felony.”

The story of the Strad is worthy of John le Carré, only with the thrill of the chase sobered by the sad strains of Tchaikovsky’s violin concerto. Totenberg remained joyous to the end, playing until two weeks before his death at the age of 101. But he rarely, if ever, spoke of the Stradivarius, his musical partner of four decades. And Johnson, full of a frustrating level of unrealized promise, seemed unwilling to commit to his craft. He headed west, to California, struggled with money and his marriage, and died at 58, of cancer.

“This, whatever his troubles were or might have been, was a very, very sad thing,” said the conductor Steven Mercurio, who was at the start of his career when he led a concert in Boston that featured Johnson as the soloist.

It took place June 6, 1980 — three weeks after the theft.

“This is not the way I want to remember somebody,” Mercurio said. “I’d rather remember him trying to play Sibelius.”

“It is sad,” Nina Totenberg said. “As the [FBI] agent said to me, that’s his one regret. That they didn’t get it back in time for him to see it and play it again. ”

The Ames Stradivarius was recovered by the FBI in June. (FBI New York)

Johnson’s act baffled Totenberg. She could not understand why he held on to the instrument. It was discovered this year by Tran, four years after Johnson’s death, when her boyfriend broke the combination lock on its case. In theory, playing it onstage would be like putting a Vermeer stolen from the Isabella Stewart Gardner Museum on your Facebook page. “An egotistical trophy,” is what Totenberg called Johnson’s decision to hold on to the violin.

But did the violinist perform and record with the Strad? Cellist Michael Fitzpatrick, who played in a trio, Mobius, with Johnson in the early 1990s, spoke Thursday of a curious habit his onetime colleague had of tucking his violin under his armpit when he carried it.

“I had never seen anyone carry a fiddle that way,” he said. “I would say to our pianist, Xak, isn’t that weird? And that was the end of it. But it may have been the violin.”

Phillip Injeian, the appraiser and instrument maker who met with Tran in late June in New York, identified the Strad and contacted the police and the FBI, said it was certainly possible Johnson played it. Would anybody really think a little-known player was using a Stradivarius?

“He certainly didn’t advertise it, because someone would have recognized it,” Injeian said. “There are a lot of copies out there. I make them myself. I take pride in making instruments that are so good that people will say, ‘Is that a Stradivarius?’ ”

Everyone knew Roman Totenberg’s path. He worked with Arthur Rubinstein, played with the Berlin Philharmonic, Boston Symphony and virtually every other major orchestra, and he performed recitals at the White House and Carnegie Hall. He headed the string department at Boston University from 1961 to 1978 and then directed the Longy School of Music in Cambridge, where the Strad was stolen.

Roman Totenberg conducts a student orchestra. (Family photo via National Public Radio)

Roman Totenberg performs with the Stradivarius in the 1950s. (Familyphoto via National Public Radio)

Johnson’s life was different. In Boston, news clippings show him featured in a 1978 chamber concert of Beethoven and Schubert at Boston University in 1978 and the Sibelius under Mercurio. In the late 1980s, Fitzpatrick met Johnson in New York. Back at the violinist’s apartment, he showed Fitzpatrick a tape he’d made of him playing Jimi Hendrix’s “Purple Haze.”

“It was bonkers, like nothing else I’d heard before,” he said. “He had chops like Paganini.”

They formed Mobius, recorded a double album and earned notice in a lengthy New York review. But Johnson frustrated his trio mates. They pleaded with him to practice. They loved his explosive skills. But he couldn’t hold a long note. He was jittery.

“We had to sit him down,” Fitzpatrick says. “We said, ‘We love you, we love your playing, but if we’re going to step on the big stage with you, you’ve got stuff in your playing you’ve got to raise the level of. It’s only going to take an hour a day. His retort was, ‘You guys are too concerned with technical perfection. Let the spirit of the music drive it.’ ”

During the summer of 1993, Johnson and Mobius went to Italy to perform in the Spoleto Festival. Mercurio, the festival’s music director, picked Johnson to serve as concertmaster of the orchestra’s grand finale concert, a performance of Berlioz. But he ultimately replaced him before the big performance.

“He was too late, too often,” Mercurio says. “And I said, ‘I can’t have my concertmaster be there too late. I don’t care how well you play the violin.’ ”

Mobius would dissolve soon after and Fitzpatrick lost track of Johnson. The violinist did play some in California. He also got divorced and, in 2007, filed for bankruptcy. But near the end of his life, Johnson had one last wish. To record Sibelius again. A cellist called Mercurio, who in the years since Spoleto has served as principal conductor of the Philadelphia Opera and recorded with artists including Andrea Bocelli and Sting.

“They said, ‘Phil’s dying. And a lot of us are going to get together because Phil’s never had a penny to his name,’ ” he said. “ ‘We’re going to give him this last wish playing Sibelius.’ ”

On Nov. 11, 2011, Johnson died in the Venice neighborhood of Los Angeles.

A Stradivarius violin was stolen from concert violinist Roman Totenberg in 1980. Now the instrument has been found and is being returned to his daughter, National Public Radio’s Nina Totenberg. (Associated Press)

For a time after the theft, Roman Totenberg held out hope. He spoke about opening his case and expecting to find his violin. Then he stopped speaking about it. He cashed in his $101,000 insurance payment, sold a few other instruments and purchased a Guarneri. Johnson wasn’t forgotten.

“My mom kept asking people if they would break into his apartment and look for the violin,” Nina Totenberg said.

For the rest of his life, Totenberg continued to meet with students and play his Guarneri. Knowing his health was failing near the end, the sisters let his network of former students know. Some drove through the night to be with him, next to his bed in Newton, Mass., playing for him.

On Thursday in New York, the media event opened with an assistant U.S. attorney, Jason Masimore, playing Bach. U.S. Attorney Preet Bharara said no criminal investigation was underway.

The sisters spoke about their plans for the violin. They have paid back the insurance company and will have the Stradivarius repaired. It will be sold, but the buyer will be selected carefully. He or she must be someone who will play it.

“Our only real sadness is that our father is not here to see this,” Nina Totenberg said. “If he were, I know he would say this is just a wonderful day. I think he’s somewhere, with my mother, celebrating, maybe drinking a shot of vodka.”