The worst thing Jack Thomas did was alter a visa in his passport. The former Melbourne taxi driver was on Thursday cleared for the second time of accepting money from Osama bin-Laden’s terrorist group al-Qaeda.

After two trials on the same charges and five years of legal battles which have affected his health, including a major depressive disorder and post-traumatic stress, Thomas has been vindicated.

“He has now been acquitted of all terrorist related charges and obviously that is a matter of great satisfaction to him and to those of us who represented him,” his lawyer Jim Kennan SC told reporters after a Supreme Court jury cleared him of accepting funds from al-Qaeda.

The same jury found him guilty of possessing a falsified Australian passport, in which he had altered the Taliban visa for Afghanistan he used to enter the war-torn country in 2001.

He feared the visa would get him a “one-way ticket to Guantanamo Bay”.

Thomas, 35, faces two years in jail for what is still a serious offence, but considering the fate he could have been dealt, the father of three was planning a “quiet” celebration with his family tonight at home in Werribee.

After converting to Islam, he went to a military camp in Afghanistan with the idealistic aim of helping bring an end to its civil war and to help in the creation of a Muslim state.

Although it didn’t get him to Guantanamo Bay, his adventure sent him to jail in Pakistan for six months, during which he was subjected to what Mr Kennan described in court as mistreatment in a “doghouse-like cell”.

After being arrested as he tried to leave Karachi airport in January 2003, Thomas told the ABC he was hooded, handcuffed, chained to the cell’s bars, strangled, suffocated, refused water and threatened with execution.

In January 2006, he was the first Australian to be convicted under new terrorism laws, and sentenced to five years jail for accepting $US3,500 ($A5,000) cash and a plane ticket home from al-Qaeda operative, Khaled bin Attash.

Those convictions were quashed by the Court of Appeal seven months later.

In December 2006, prosecutors successfully sought a retrial following evidence Thomas revealed in interviews to the ABC and The Age newspaper.

For seven days from last Tuesday, the retrial was told the details of his time in Afghanistan he recounted to ABC journalist Sally Neighbour for ABC current affairs program Four Corners.

It wasn’t until explosions and bullets erupted, heralding the arrival of bin Laden into the Afghan mountain camp, he said, that he realised he was not just at any old military camp, but an al-Qaeda camp.

There was a festive atmosphere when bin Laden visited, which he did three times during 2001 when Thomas was at the camp.

Rocket-propelled grenades were launched into the side of mountains, explosions and anti-aircraft fire clouded the air, bullets were fired.

And Thomas got close enough to bin Laden to observe the al-Qaeda leader was polite and shy, didn’t mind a hug, but wasn’t so fond of kissing.

“He was definitely well loved,” Thomas said of bin Laden in the interview. “(He) was very polite and humble and shy.

“He didn’t like too many kisses. He didn’t mind being hugged, but kisses he didn’t like.”

Thomas said bin Laden “seemed to float across the floor”.

In the interview, the Muslim convert told Neighbour that at the camp he felt “like a king, Robin Hood, as part of a band of merry men”.

The court also heard from Fairfax Media journalist Ian Munro, who interviewed Thomas in 2006.

Thomas told Munro he went to Afghanistan in March 2001 because he wanted to help bring about peace in the country and aid in the creation of a Muslim state.

Thomas intended to go to a Kurdish camp to train to fight on the frontline, but told Munro he was redirected to al-Farouk.

Thomas admitted to Neighbour he didn’t know the camp he ended up at was operated by al-Qaeda.

“(I) later found out the camp to be an al-Qaeda camp,” he said in the ABC interview.

Asked if he knew it was one of bin Laden’s camps, Thomas replied: “At the start, no, not until he arrived on the first occasion.”

The third time bin Laden visited, Thomas said the al-Qaeda leader told the camp “something big was going to happen”.

At the time, the camp trainees were evacuated to the mountains every night and there was a fear the “something big” was an attack on Afghanistan, Thomas said.

Asked by Neighbour whether he thought bin Laden’s reference to “something big” was to the attacks on the United States on September 11, Thomas responded: “In hindsight.”

Thomas said when he had learnt about the attacks, he felt shock and disbelief.

He escaped into Pakistan after the attacks and it was during his time there that the prosecution alleges Thomas accepted the cash and ticket home from bin Attash.