By Syed Shoaib Hasan
BBC News, Islamabad
Siddiqui maintained the charges against her were fabricated
Despite anger in Pakistan, the conviction of Pakistani doctor Aafia Siddiqui in a US court for the attempted killing of US agents is not going to come as a surprise to anyone.
Her supporters and family here have been vociferous in their protests against her trial, but even they were not hopeful about the outcome.
"We were expecting this," Siddiqui's uncle, Shamsul Hasan Farooqi, told the BBC.
Other family members were equally indignant.
"My sister is innocent - she has been tortured and detained for years," Dr Fauzia Siddiqui said.
"She is a victim of American injustice."
The jury at the New York court was unanimous in its verdict.
But the trial has far from resolved the many questions surrounding Siddiqui since her disappearance from Karachi on 30 March 2003.
On that day she drove out of her home with her three children and was not heard of again until 14 July 2008 when she was produced in front of a group of journalists in the province of Ghazni in Afghanistan.
Five unaccounted years
What happened in those five years is the subject of much speculation.
Afghan security officials said in 2008 that she had been arrested while planning to carry out "a terrorist attack".
The authorities said she was carrying containers of unidentified chemicals and notes referring to "mass-casualty attacks" in New York.
While she was being questioned by US special agents in Afghanistan, US officials said she took up an unattended rifle and shot at the agents.
Although none of the US soldiers or agents in the room was injured in the incident, Siddiqui herself was shot.
She was subsequently flown to New York to be tried for the attempted murder of US officials. She was never charged in connection with any terrorist offences.
But Siddiqui's family denies this version of events.
They say she was kidnapped in Karachi along with her children and then kept in a secret US prison.
They point to the fact that Siddiqui was only "arrested" after an outcry about her alleged detention in Afghanistan's Bagram airbase.
Reports of her presence there were initially made by British journalist Yvonne Ridley - best known for her capture by the Afghan Taliban in 2001 and her subsequent conversion to Islam.
Siddiqui herself appeared to suffer from memory loss after she was taken to New York for the trial in August 2008.
It is alleged Siddiqui ended up at Bagram air base
She later said she had been detained at a US secret prison but could not recall the details.
But there are facts about the case itself which puts all these claims in a different light.
Siddiqui divorced her first husband and is then said to have married Amar Al Baluchi.
He is the nephew of Khalid Sheikh Mohammad, the main planner of 9/11.
Whether she came under his influence is unclear. Both men are currently on trial in the US.
Mystery also surrounds the fate of two of Siddiqui's three children.
In 2008 Siddiqui's eldest son was handed over to Pakistani officials by Afghan authorities.
She also has another son and daughter - but their current whereabouts are unknown.
The only real clue to all these may lie in what her uncle, Shamsul Hasan Farooqi has said. His account first appeared in The Guardian newspaper but he has now told the BBC about her state of mind when he saw her last in 2008.
"Five years after she went missing, my niece reappeared on my doorstep on 22 January 2008," he said.
"Someone had rung my door bell and then my servant came and told me a woman wanted to see me.
"When I went to meet her, I saw Aafia standing outside. She was wearing a burka and was clearly very scared.
"She said she wanted me to put her in touch with the Afghan Taliban."
Mr Farooqi explained that he used to carry out geological work in Afghanistan and had established contact with the Taliban in 1999.
Siddiqui grabbed a rifle and opened fire on US agents, the court heard
"But I told her that I was no longer in touch with them," he said.
Mr Farooqi said that his niece also spoke about what happened after she went missing - he was told that she had been "held in various places at various times".
"She had not seen her children for years - sometimes her captors said they were dead and sometimes that they had been sent abroad," he said.
"She was quite clear that she was being held by Pakistani agencies. She spoke well of the Americans, but was clearly afraid of the Pakistanis.
"Before she came to see me, she said that she was being held in Lahore by a security agency."
Mr Farooqi says that he immediately called his sister - Siddiqui's mother - who flew in from Karachi the next day to meet her daughter.
He says Siddiqui stayed with them for two days.
"Throughout this time I had a strong feeling that she was being monitored in some way - through a device on her person or some other method," he said.
When contacted by the BBC, her sister Dr Fauzia Siddiqui refused to comment on this account. But she had earlier denied it in an interview with The Guardian newspaper.
On the basis of this account and other reports of Siddiqui being sighted in Pakistan's north-western tribal region, a different picture emerges.
"It could well be that Dr Siddiqui was working as a double agent after her disappearance," says a journalist who has investigated the case.
"But she may have eventually decided enough was enough and rejoined the jihadis."
She certainly would not be the first person to do so - a recent deadly attack in Afghanistan which killed seven CIA agents was reportedly carried out by an al-Qaeda double agent.
Much remains murky about the life of Siddiqui and it looks as if many of her secrets will go to jail with her.