Erol Incedal twice stood trial on terrorism charges. Last year he was convicted of possessing a bomb-making manual, but the jury failed to reach a verdict on the more serious charge of plotting a terrorist attack. After a four-week retrial, he was acquitted of that charge on Thursday.

On each occasion, the evidence was carefully presented in one of three sessions. Parts of the case were in open court, with the press and the public free to come and go; other parts were held behind locked doors, before a jury whose members were warned that they could go to jail if they ever divulged what they had heard; and parts were held in intermediate sessions, in the presence of the jury and a small group of journalists who are prohibited – at least for the time being – from reporting what they learned.

As a consequence, members of the public have no idea what lay at the heart of the prosecution of Incedal; nor the evidence that resulted in the jury clearing him of plotting terrorist attacks.

The media is not allowed to explain why a man who was found guilty of possessing a bomb-making manual was not convicted of preparing acts of terrorism. Incedal claimed to have a “reasonable excuse” for carrying the document around with him. What was that excuse? By law, and on pain of prosecution, that small group of journalists who know the answer cannot disclose it.

Nor, currently, can the public be told why all these matters are being concealed from them, or by whom.

Erol Incedal was acquitted of plotting a terror attack. Photograph: Facebook

While the jury heard all the evidence, the crux of the case of R v Erol Incedal remains an official secret as far as the wider public is concerned.

These unprecedented arrangements were imposed on the trial judge, Sir Andrew Nicol, by the court of appeal. Nicol had originally acceded to a demand from the prosecution that the entire trial be heard in secret, and that Incedal, and the man arrested with him, Mounir Rarmoul-Bouhadjar, be identified only as AB and CD.

The Crown Prosecution Service had maintained there was a serious possibility that the prosecution could not go ahead unless these measures were in place. The reasons for that claim cannot currently be reported. However, the appeal court’s judgment, a public document, noted that national security was “the raison d’etre” of MI5 and MI6, and that “from time to time, tensions between the open justice principle and national security will be inevitable”.

So unusual was the proposed departure from the common law principle of open justice that it was denounced by MPs and civil rights group Liberty as dangerous and draconian; lawyers representing a dozen media organisations, led by the Guardian, mounted a challenge.

Mr Justice Nicol, the trial judge. Photograph: David Wimsett/Photoshot

This led to the court of appeal ruling in June last year that that while “the core of the case must be in camera”, a number of journalists selected by the media organisations behind that challenge should be “invited to attend the bulk of the trial”.

After hearing further submissions from crown prosecutors, thre defence and lawyers representing the media, Nicol will now review the secret evidence and decide what may be made public.

Throughout each of those intermediate sessions, the small number of journalists allowed into court nine at the Old Bailey were expected to surrender their mobile phones, which were locked in soundproof boxes. At the end of each session, the journalists were obliged to hand their notebooks to a police officer, to be locked in a safe at the back of the court.

Police officers watched closely to ensure the journalists did not attempt to remove any notes from the court. There was a comic moment when a detective accused the man from the Express of surreptitiously making a second set of notes and attempting to smuggle them out. The journalist dutifully handed over the crossword he had been completing during lulls in the proceedings.

After the jury retired to consider its verdict, the journalists were told they would not be permitted to remove their notebooks from court unless certain words were “completely excised” from their pages. The identity of the people responsible for making this demand cannot currently be reported. After Incedal’s acquittal, the police officers in court told the reporters that they may never see their notebooks again.

Whenever the court went into a fully secret session, one of the police officers would lock the doors from the inside. Nicol told the jury that the evidence heard during these sessions would never be made public.

Although the journalists were not threatened with imprisonment, the implication was clear: if they breached the reporting restrictions, they would be held to be in contempt of court, and could face prosecution.

Many of the journalists found the process objectionable. Sean O’Neill, crime editor of the Times, described it as “a deeply unhealthy process”, adding: “In my view there was very little in those sessions that should have been kept secret but an awful lot that should have been exposed and scrutinised.”

The restrictions did not end at the exit from court nine. The reporters were warned that if they wished to take legal advice about the case, and the secret evidence that they had heard, they could do so only in “a confidential meeting”.

This was defined in a court order handed down by Nicol as “a meeting that takes place in a room in which the door is closed and it is clear that no one can overhear from outside the room what is being said during the meeting”. The order further stipulated that “mobile phones must be switched off and any telephone landlines must not be connected [ie the line open] to any internal or external other telephone. No part of the meeting can be recorded and no notes made.”

A proposal that the order should also decree that the door to the meeting room should be locked, and that there should be no CCTV in the vicinity, was dropped.

If Nicol does lift the reporting restrictions on significant parts of the secret evidence, parliament and the public will be able to judge for themselves whether the open justice principle was torn up in the case of R v Erol Incedal to protect national security.

It may be that there will then be questions for Theresa May, the home secretary, and William Hague, the former foreign secretary, each of whom signed ministerial certificates supporting the application for all-embracing secrecy.

There may also be questions asked of the crown prosecutors who had insisted on the need for complete secrecy, and of those instructing them, on whose behalf this demand was made.

As a consequence of the reporting restrictions, and the way in which the evidence was carefully divided between the three parts of the trial, the identity of those instructing the prosecution is also currently hidden from view.