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In a letter published by Egyptian newspaper al-Masry al-Youm, Mohamed Fahmy, the al-Jazeera English journalist imprisoned in a Cairo jail fro over a year, and released today on bail, highlights the risks and difficulties faced by journalists for just doing their job.

“A journalist dedicates his life to covering stories and faces the hardest conditions and situations,” Fahmy, 40, wrote in October 2014.

“But when he becomes the story overnight, then there must be a mistake.”

Fahmy, along with fellow al-Jazeera journalists Peter Greste and Baher Mohamed, has been at the centre of the story for more than a year. Accused of being members of the Muslim Brotherhood, as well as broadcasting false news, the three were found guilty in June 2014 after a trial riddled with inconsistencies, and sentenced to multiple years in prison.

Fahmy has repeatedly insisted that the dispute between Egypt and Qatar following the coup against former president Muhammed Morsi in June 2013 was the reason behind the trumped up charges against him.

Qatar had been one of Egypt's main backers in the Morsi's period in office, but that financial support ended once General Abdel-Fattah al-Sisi, now President Sisi, took over. What followed was the demonisation of Qatar in Egypt, and Saudi Arabia and the United Arab Emirates, Doha's local rivals, stepping up to fill in the gap left by Qatar's largesse.

While Greste, who was deported from Egypt on December 1, and Mohamed largely stayed silent on the geopolitical machinations, Fahmy was vocal.

In a message delivered to the Canadian Journalists for Free Expression Gala in December, Fahmy said that the al-Jazeera journalists were “victims of a real ongoing cold war between Egypt and Qatar”.

“Egypt decided to teach Qatar a lesson for continuing to support the Muslim Brotherhood as Doha welcomed many wanted Islamist fugitives pursued by Egypt,” Fahmy said. “Qatar had also withdrawn their much-needed $10 billion in bonds from Egyptian banks... In retaliation, Egypt decided to punish Mohamed Fahmy, Peter Greste and Baher Mohamed in their score-settling with this ambitious nation, Qatar.”

Fahmy's disbelief at what has happened to him is compounded by his opposition to the Muslim Brotherhood, something that he has emphasised on numerous occasions.

Egypt decided to punish Mohamed Fahmy, Peter Greste and Baher Mohamed in their score-settling with this ambitious nation, Qatar. - Mohamed Fahmy

Ironically, he seems to have welcomed the coup against Morsi and the Brotherhood. Writing from his prison cell, he describes joining the protests against the group in the days before the coup, and his joy at seeing the Egyptian air force “draw hearts in the skies of Cairo” in support of the protests.

“We had to eradicate this Brotherhood cancer from its roots like we did on June 30 to save the patient [Egypt] from death,” Fahmy wrote.

Fahmy was perhaps trying to curry favour with Egyptian establishment with these statements, and he has certainly had support from prominent figures such as Amr Moussa, but they quite clearly reflect how bizarre the accusations against him are – and the betrayal he must feel at a new order that he had welcomed.

Fahmy has not been particularly vocal in his criticism of al-Jazeera, who he only joined months before his arrest, but the fact that he now has a separate legal team to his fellow al-Jazeera detainees is telling.

Mohannad Sabry, a journalist who worked with Fahmy in the past, in which he made several claims against al-Jazeera English, implying that the management made several mistakes in the run up to Fahmy, Greste, and Mohamed's detention, and accusing the organisation of failing to protect its journalists.

According to Sabry, one of Fahmy's main concerns upon taking the job was the association with the banned al-Jazeera Mubashir Misr, the network's Arabic-language Egyptian affiliate, which was seen to have a pro-Muslim Brotherhood bias.

“This is AJ English, we have nothing to do with Mubashir Misr and their issues with the government,” Sabry said that Fahmy told him. Later on Fahmy was angered to see that his team's reports had been translated and aired on Mubashir Misr.

Fahmy himself said that he had taken the job despite knowing that he was sailing into a storm and faced “ferocious political waves” because of Qatar's ownership of al-Jazeera.

“Unfortunately, several months later it became evident that I had inherited a sinking ship,” was Fahmy's damning indictment. “I fired many warning flares and SOS messages as captain of this doomed ship but we kept bobbing in the ocean with no compass or a watchtower back at headquarters in Qatar to look out for our safe path.”

Al-Jazeera English has consistently defended Fahmy, along with Greste and Mohamed, labelling the charges against them as “false and baseless”, and has kept the pressure on Egypt up with a relentless media campaign calling for their release.

The al-Jazeera trio's detention is only one part of Egypt's continued suppression of any opposition to the authorities, with journalists and opposition activists finding themselves behind bars and facing life and even death sentences.

On February 2 Amnesty International labelled the sentencing of 183 people to death as “a further sign of Egypt's disregard for national and international law”.

Yet, at least from his statements delivered from prison, it appears that Fahmy believes that if he were not caught up in the dispute between Egypt and Qatar, he would have been a free man.