On Saturday Bradley Manning will mark his 1,000th day imprisoned without trial. In the course of those thousand days, from the moment he was formally put into pre-trial confinement on 19 May 2010 on suspicion of being the source of the WikiLeaks disclosures, Manning has been on a long and eventful journey.

It has taken him from the desert of Iraq, where he was arrested at a military operating base outside Baghdad, to a prison tent in Kuwait. From there he endured his infamous harsh treatment at Quantico Marine base in Virginia, and for the last 14 months he has attended a series of pre-trial hearings at Fort Meade in Maryland, the latest of which begins next week.

For the small band of reporters who have tracked the prosecution of Private First Class Manning, the journey has also been long and eventful. Not in any way comparable, of course; none of us have been ordered to strip naked or put in shackles, and we have all been free to go home at night without the prospect of a life sentence hanging over us.

But it's been an education, nonetheless. Though we are a mixed bag – a fusion of traditional outlets such as the Washington Post and Associated Press and new-look bloggers such as Firedoglake and the Bradley Manning support network – we have been thrown together by our common mission to report on the most high-profile prosecution of an alleged leaker in several decades.

There's something else that binds us – disparate though our reporting styles and personal politics might be – and that's the daily struggle to do our jobs properly, confronted as we are by the systemic furtiveness of the US government. It's an irony that appears to be lost on many of the military lawyers who fill the courtroom at Fort Meade. A trial that has at its core the age-old confrontation between a government's desire for confidentiality and the public's need to know, is itself being conducted amid stringent restrictions on information.

None of the transcripts of the court martial procedure have been released to us. No government motions to the court have been published. David Coombs, Manning's lead lawyer, has had to plead to be allowed to post his defence motions, and when he has been granted permission he has often been forced to redact the documents to an almost comical degree.

The most egregious example of this over the past 1,000 days was the moment in January when the military judge, Colonel Denise Lind, issued her ruling in an Article 13 motion brought by Manning's defence. This was the complaint that the soldier, while at Quantico, had been subjected to a form of pre-trial punishment that is banned under the Uniform Code of Military Justice.

It was an important moment in the narrative arc that is the Bradley Manning trial. Technically, Lind had the power to dismiss all charges against the soldier; she could have, though none of us expected that she would, let him walk out of that court and into freedom. (In the end she knocked 112 days off any eventual sentence).

The accusations contained in the Article 13 also went to the heart of the defence case that Manning was singled out for unfair and at times brutal treatment. During the testimony, Manning himself gave evidence, standing inside a 6ft by 8ft (180cm by 240cm) box that had been drawn on the floor of the courtroom to replicate the dimensions of his cell. He recalled such humiliating details as the routine he was required to follow when he needed toilet paper. Standing to attention at the front bars of his cell, he was ordered to shout out to the guards who kept him under 24-hour observation: "Lance Corporal Detainee Manning requests toilet paper!"

So my fellow reporters and I awaited with intense interest Lind's judgment, though also with some trepidation. We'd sat through the spectacle of Lind reading out to the court her rulings, and it wasn't a pleasant experience. The judge has a way of reading out her decisions at such a clip that it is almost impossible to take them down even with shorthand or touch typing.

In the event, Lind spent an hour and a half without pause reading out a judgment that must have stretched to 50 pages, at a rate that rendered accurate reporting of it diabolically difficult. No copy of the ruling has – then or now – been made available to the public, presumably on grounds of national security, even though every word of the document had been read out to the very public that was now being withheld its publication.

Such is the Alice-in-Wonderland world of the Bradley Manning trial. Why does it matter? It matters to Bradley Manning. The soldier is facing charges that carry the stiffest punishment available to the state short of killing him. (They could technically do that to him too, but the prosecution has made clear it will not seek the death penalty). If found guilty of the most serious charge – "aiding the enemy" – he could be confined to military custody for the rest of his life with no chance of parole, a prospect that makes the past 1,000 days look like a Tea Party.

The least Manning deserves is stringent fairness in his prosecution, and stringent fairness cannot exist in the absence of openness and transparency. As a British appeal court judge wrote in a recent case brought by the Guardian to protest against excessive courtroom secrecy: "In a democracy, where power depends on the consent of the governed, the answer must lie in the transparency of the legal process. Open justice lets in the light and allows the public to scrutinise the workings of the law, for better or for worse."

There's a much bigger reason why the cloak-and-dagger approach of the US government to this trial should be taken seriously. America doesn't seem to have woken up to this yet, but the prosecution of Bradley Manning poses the greatest threat to freedom of speech and the press in this country in at least a generation.

The "aiding the enemy" count essentially accuses Manning of handing information to Osama bin Laden as a necessary consequence of the act of leaking state secrets that would end up on the internet. When one of the prosecution lawyers was asked whether the government would still have gone after Manning had he leaked to the New York Times instead of WikiLeaks, she unhesitatingly replied: "Yes".

If that's not a threat to the first amendment, then what is? This prosecution, as it is currently conceived, could have a chilling effect on public accountability that goes far beyond the relatively rarefied world of WikiLeaks.

That's something worth contemplating as Bradley Manning enters his second 1,000 days sitting in a cell. Looked at this way, we're sitting in the cell with him.