An FBI agent who was one of the leads on the initial 9/11 investigation believes the evidence of possible Saudi links is significant and should be publicly released.

A team of FBI agents spent more than a decade secretly investigating the possible Saudi links - even after they were told to give up and high-level officials disregarded any connections.

The details regarding the FBI investigation - dubbed Operation Encore - has mostly been shrouded in secrecy since the terror attacks occurred in 2001.

A joint investigation by New York Times Magazine and ProPublica - that included interviews with over 50 current of ex-FBI agents - has uncovered several missed investigative opportunities.

As a result, the agents say they were ultimately unable to fully pursue potential links that may have provided smoking gun evidence that Saudi Arabia was involved somehow.

Richard Lambert, who was the San Diego lead on the FBI's initial 9/11 investigation, believes the evidence of possible Saudi links is significant enough and should be publicly released - even though it's not conclusive.

'The circumstantial evidence has mounted,' he said.

'Given the lapse of time, I don't know any reason why the truth should be kept from the American people.'

Among the missed opportunities to follow up with included Saudi men Omar al-Bayoumi (left) and Mohdar Abdullah (right) who both had contact with the hijackers prior to the 9/11 attacks

The Justice Department last year refused to hand over investigative files to the families of 9/11 victims despite a promise from President Trump (pictured at the 9/11 memorial at the Pentagon last year)

The Justice Department last year refused to hand over investigative files to the families of 9/11 victims despite a promise from President Trump.

He had vowed to help the families after they visited him at the White House last year during a 9/11 memorial service and begged him for help so they could get closure.

The families, who were told Trump had ordered the Justice Department to release the name of a Saudi diplomat linked to the attacks, planned to use the files in a lawsuit accusing Saudi of being involved.

Attorney General William Barr later informed that families in court that all other files had to be protected as state secrets.

Among the links uncovered in the investigation included Saudi men Omar al-Bayoumi and Mohdar Abdullah who both had contact with the hijackers prior to the 9/11 attacks.

Bayoumi - a Saudi student living in Southern California at the time - may have had prior knowledge of the 9/11 attacks, agents revealed.

The FBI found Bayoumi had connections to two of the plane hijackers - Khalid al-Mihdhar and Nawaf al-Hazmi - who crashed Flight 77 into the Pentagon.

He was a co-signer on the hijacker's apartment in San Diego when they arrived in the U.S. prior to the 9/11 attacks.

Bayoumi was also paid a stipend by the Saudi government while in the U.S., which came from a Saudi contracting company. That stipend increased at the time he was helping the hijackers but agents found no evidence he was financially helping them.

Investigators also found that a friend of Bayoumi's wife, who was a Saudi woman living in San Diego, also received $70,000 from the wife of Prince Bandar - a Saudi ambassador to the U.S. They later determined that the Bandars regularly gave month to Saudi expats.

Bayoumi was living in the UK with his wife and children when the FBI went to question him in the wake of 9/11.

The agents had to question him via British detectives and he was eventually freed without the FBI ever having a chance to ask him if he had a relationship with Saudi intelligence.

Among the evidence seized from his UK home was a spiral notebook that included a drawing of a plane striking the ground.

Investigators found the plane's descent was like the one that Flight 77 did when it hit the Pentagon.

Some agents argued the diagram proved he knew about the attacks prior, while others argued the document's significance was unclear.

Joseph Foelsch, a former investigation supervisor, said it may have had more weight if it had been discovered right after 9/11.

'That would have been harder evidence,' he said. 'If not a smoking gun, a warm gun.'

Bayoumi moved back to Saudi Arabia in 2002 and the U.S. revoked his visa for 'quasi-terrorist activities'.

Khalid al-Mihdhar (left) and Nawaf al-Hazmi (right) were the two hijackers who took control of Flight 77 and crashed it into the Pentagon in the 9/11 terror attacks

The details regarding the FBI investigation - dubbed Operation Encore - has mostly been shrouded in secrecy since the terror attacks occurred in 2001

When he was questioned again in 2004 in Saudi, Bayoumi said he met the hijackers by chance and argued he was a hospitable Muslim by helping them find accommodation.

The FBI officially ruled Bayoumi's help to the hijackers was unwitting and put it down to a 'random encounter'.

Mohdar Abdullah, a Saudi man living in San Diego, was also among those embroiled in the post 9/11 FBI investigation.

Agents received a tip that they should speak to Abdullah after the attacks and they tracked him down about two weeks later at San Diego State University.

'What took you so long?' Abdullah is said to have asked the FBI agent. 'I thought you'd be all over me sooner.'

He told the FBI that he was introduced to the hijackers by Bayoumi who had asked him to help the two men settle into life in San Diego.

Abdullah went on to give the FBI agent information about the hijackers' lives in San Diego in the lead up to the attacks.

He told the agent he'd tried to organize them flying lessons in May 2000, drove them on errands and enrolled them in English lessons.

When Abdullah refused to take a polygraph test, authorities arrested him and he was flown to New York to be put before a grand jury.

He never ended up being charged in connection to the attacks. He was, however, charged with immigration fraud for lying on his initial visa application about his birth country.

Abdullah was jailed for two years in a federal prison and risked being deported when he was released.

FBI agents had by then received tips that Abdullah may have had advanced knowledge of the 9/11 attacks, including from two former prisoners who said he admitted to knowing about the attacks.

The Justice Department refused to delay his deportation and he was sent back to Yemen in May 2004.

When the FBI learned Abdullah had applied for a Canadian visa in 2006, the U.S. agents tried to speak with him again and hatched a plan to convince him to speak.

In the years since they first questioned him, the FBI had learned that Abdullah had married a 16-year-old Puerto Rican girl the night before the 9/11 attacks in a Denny's carpark because he believed it would grant him U.S. citizenship.

The pair consumated the marriage before he was arrested 11 days after the attacks.

In a bid to gain his trust, the FBI agent doctored a photo of a child and told Abdullah that it was his five-year-old child.

'I knew I had a kid!' he said.

Abdullah went on to give the agent more information about the hijackers that led authorities to identify two more people who had contact with the hijackers in the weeks before the attacks.

He later moved to Sweden and refused to be a cooperating witness for the FBI.