A missing teenager, an empty tomb, a swirl of dark theories, and the closed doors and habitual secrecy of the Vatican. It sounds like fiction, but it is a real-life mystery that has gripped Italy for more than three decades and has embroiled the powerful and inscrutable Holy See.

For 36 years, the family of Emanuela Orlandi has sought answers about the fate of the 15-year-old girl who vanished from the streets of Rome on her way to a flute lesson.

Yesterday, in the presence of an expert appointed by the Orlandi family, forensic scientists extracted bones from two ossuaries found last week under a stone slab in a Vatican college. The Vatican said the bones would now be analysed to try to establish their identities.

It is the latest twist in the search for Emanuela which has so far yielded almost no clues, let alone hard facts.

“I am incapable of accepting injustices, but especially when it involves my sister, knowing that over all these years there are people who know what happened,” Pietro Orlandi, her older brother, told the Observer. “For me, the right to the truth and the right to justice are sacred rights that nobody can ever take away.”

Facebook Twitter Pinterest The opening of two tombs at the Pontifical Teutonic Cemetery last week as part of the investigations into the disappearance of teenager Emanuela Orlandi. Photograph: EPA

Pietro and his four sisters had a happy childhood inside the historic Vatican City, where his father was a lay employee in the papal household. “The Vatican gardens were available to us as if it was our own back garden. We felt we were in the safest place in the world,” he said.

On 22 June 1983, Emanuela left the family home, carrying her flute. She had asked her brother to accompany her on the bus to her music class a mile away, but Pietro had other commitments. “It’s a very painful memory – she insisted I take her, and we rowed over it. Then she left, slamming the door. I never thought it would be the last time I saw her. I’ve gone over it so many times, telling myself if only I had accompanied her maybe it wouldn’t have happened.”

Later, Emanuela called home, speaking to one of her sisters. Since then, there has been no trace of the teenager, and Italian investigators have been unable to reach a conclusion about what happened to her.

Facebook Twitter Pinterest Pietro Orlandi, Emanuela’s older brother, in Rome last week, still searching for clues. Photograph: Andreas Solaro/AFP/Getty Images

“From that day, my family entered into this nightmare,” said Pietro. They discounted any suggestion that Emanuela had left of her own accord. “She was so serene, she had something planned with her sister and had music recitals a few days later.”

The family thought Emanuela may have been abducted or involved in an accident. “Then Pope John Paul II made an appeal during his angelus. That unleashed everything. Emanuela was all of a sudden at the centre of an international intrigue.”

Rumours circulating over the following years linked Emanuela’s disappearance with a 1981 plot to assassinate the pope, a wave of financial scandals at the Vatican bank, an alleged sex ring run by Vatican police, and Italy’s criminal underworld.

In 2012, police exhumed the body of Enrico “Renatino” De Pedis, a mobster who had been buried in the crypt of Sant’Apollinare basilica in Rome. No link with Emanuela was discovered, and De Pedis’s remains were cremated and scattered at sea.

Two years ago, an Italian investigative journalist published a five-page document that had purportedly been written by a cardinal and held in a locked Vatican cabinet. It suggested the Holy See had been involved in Emanuela’s disappearance. The document was a fake, the Vatican said.

“I don’t know about the theories,” said Pietro. “But I do say this: the behaviour of the Vatican over these 36 years has been one of secrecy and lack of collaboration, and it has made me think there are leaders within the Vatican who know what happened.

Facebook Twitter Pinterest The body of mobster Enrico De Pedis was exhumed in 2012 but no link to Emanuela was found. Photograph: EPA

“From John Paul II to Ratzinger [Pope Benedict XVI] and Pope Francis, they all know what happened. But due to this being so damaging to the image of the church, they’ve been doing all they can to ensure that the truth doesn’t come out.”

Ten days ago, two tombs at the Pontifical Teutonic cemetery in the Vatican were opened after an anonymous letter to the Orlandi family containing a photograph of a stone figure in the cemetery advised them to “look where the angel is pointing”.

But the tombs were empty – not only of Emanuela’s remains but also those of two 19th-century German princesses who had been buried there. Conspiracy theories were fuelled by a Facebook message posted by Francesca Chaouqui, a PR consultant convicted in 2016 of leaking classified Vatican documents to journalists. “I told Pietro the tombs would be empty. This is my only statement on the matter,” she wrote. “I will not be able to add any details … until I am released from the [code of] pontifical secrecy.”

Yesterday it was disclosed after it had been opened that an underground space inside the Pontifical Teutonic College, which had been covered by a manhole, holds thousands of bones that appear to be from dozens of individuals, both “adult and non-adult”.

Emanuela and Pietro’s father died in 2004 without knowing what happened to his second-youngest child. Their mother, Maria, still lives inside Vatican City, the world’s smallest state.

“My mother is 88, and she has every faith in all I’m doing,” said Pietro. “She prays for me as she believes I will find out what happened to Emanuela, where she is or if she’s dead, and if so, where her body is. Until we find [her remains], we must never stop hoping she’s still alive.”