After more than three years, two inquiry reports and an Old Bailey trial, the inquest of Jean Charles de Menezes was supposed to end the rumours, conspiracies and misunderstandings.

It was going to be modern, open and hugely expensive. Justice would be done, and would be seen to be done.

Conference space was hired at the Oval cricket ground to accommodate the battery of lawyers and provide enough room for any member of the public to attend. The Long Room, usually the preserve of Surrey members, was set aside as an overspill area and media annexe.

But in the last days of the hearing that commitment to transparency and fairness seemed to become lost in an atmosphere of increasing acrimony.

The turning point was the decision of Sir Michael Wright, QC, the Assistant Deputy Coroner of Inner South London, to exclude unlawful killing from the verdicts available to the jury. It prompted the de Menezes family to withdraw from the process and criticise it as a whitewash.

The jury, which deliberated over its verdict for seven days, restored some of the de Menezes family’s faith yesterday by returning findings that were highly critical of the police on the day of the shooting.

Jurors opted for an open verdict but spelt out in answers to questions set by the coroner that they did not believe some police witnesses about what happened in the Northern Line carriage of the London Underground in which Mr de Menezes died.

Azad Rehman, of the Justice4Jean campaign, said that the jury had been gagged from expressing their true conclusions. “Yet the jury have come back with a damning critique of the police and its failures,” he said.

“The jury clearly said that the police lied, that Jean was completely innocent and that from the time Jean entered Stockwell Tube station, he was doomed to be shot without warning. It is clear that if they were given the option of an unlawful killing verdict, they would have reached an unlawful killing verdict.”

The continued dissatisfaction of the family and its supporters almost certainly means that further legal battles lie ahead. There will be a High Court attempt to reinstate an unlawful killing verdict, raising the possibility of another inquest. A claim for compensation is almost inevitable.

The tragedy seems likely to remain a political football, overshadowing the deaths of the 52 people murdered by terrorists on July 7, 2005, whose inquests have yet to be convened.

The Stockwell inquest, as it was officially titled, opened on September 22 to general approval and for weeks everything seemed to be going unexpectedly smoothly. More than 40 police officers gave evidence anonymously, including “Charlie 2” and “Charlie 12”, the two officers of the specialist firearms unit of the Metropolitan Police, who shot Mr Menezes dead on July 22, 2005.

The officers had not faced a public examination before and the de Menezes family, through its powerful legal team, was allowed to ask any questions. Michael Mansfield, QC, the family’s counsel, cross-examined the firearms officers, the surveillance teams, Mr de Menezes’s fellow passengers and the senior Met officers who commanded the botched operation.

Deputy Assistant Commissioner Cressida Dick, who had been cleared of any blame by an Old Bailey jury last year, looked uncomfortable in the face of Mr Mansfield’s relentless cross-examination.

As witnesses spoke, documents to which they referred appeared on large screens around the court and in the annexe. Everyone could see the police officers’ notes, the pictures of Hussain Osman, the real fugitive, which were not given to the surveillance team, the crude stick-man drawing showing the position of Mr de Menezes’s body on the carriage floor and the pathologist’s diagram of where seven dumdum bullets hit his head.

Anyone following the case from afar could access a website that carried full transcripts of each day’s hearing.

The sense of a sound legal process lasted until the penultimate week, when the one verdict that the de Menezes family and its supporters had wanted was struck out. It was also the verdict that had been dreaded but gloomily expected at senior levels in Scotland Yard.

When Sir Michael ruled it out in the first hour of his summing up, he was acting within the Coroners Rules. But the impression given, in such a sensitive and highly publicised inquest, was that the freedom of the jury to make their own decision was being severely restricted.

One de Menezes supporter asked: “If a coroner in Oxford could rule that a British army soldier was unlawfully killed by ‘friendly fire’ in Iraq, why is a jury in London not allowed to consider the same finding?”

Sir Michael, 76, a former High Court judge, who was brought out of retirement to preside over the hearing, caused further concern as he continued with his lengthy summing up.

He told the jurors to put aside emotional feelings for Maria Otone de Menezes, the dead man’s mother, who came from Brazil to hear much of the evidence. The following day, however, Sir Michael chose to remind the jury that one of the firearms officers had broken down during his evidence. “This fact may assist you in assessing the depth of the emotional experience that he was going through here when he was reliving the terrible events of July 22,” he said.

Many of the de Menezes family’s supporters were not in court to hear that remark. It can only now be reported that they had gone to the High Court, where Mr Mansfield was seeking to challenge Sir Michael’s decision to rule out an unlawful killing verdict.

The attempt to reinstate such a verdict was adjourned but Mr Justice Silber rejected a request to broaden the range of questions put to the inquest jury.

On Thursday last week, the court assembled to be told that the de Menezes family no longer wanted to participate in the process.

“This is in the light of all the rulings and restrictions placed upon the verdict or verdicts that the jury may return,” Mr Mansfield said, in the jury’s absence. Its members were not told of Mr Mansfield’s reasons for withdrawing.

Lawyers for the Metropolitan Police and its senior officers had argued that no explanation should be given. Richard Horwell, QC, for the Met Commissioner, said: “The less said, the better.”

The coroner agreed and then, in a surprise move, ordered that because of the “sensitive” situation all members of the public be removed from the courtroom before the jury were admitted.

His officials demanded that the de Menezes family, the public and the press leave the court. None budged and tempers flared. The court’s private security guards – men in grey suits, with earpieces and cuff microphones – reacted nervously to the idea of forcibly evicting the cousins of Mr de Menezes.

The coroner, meanwhile, had retreated to his room for a lunch of sandwiches, crisps and fruit, offered to him and all counsel, at a cost of £16.50 each, by the Oval catering team.

In Sir Michael’s absence, a compromise was reached in which the press and family members were allowed to remain in court but other members of the public retreated to the annexe. The coroner returned and began the hearing before family members could resume their seats, provoking protests and a noisy scuffle in the corridor.

Once inside, the family did not remain seated for long. Shortly after the jury was admitted, the cousins of Mr de Menezes removed their coats and stood to reveal T-shirts bearing the slogan “Unlawful Killing” before walking from the room. Their disenchantment, rather than a glossy façade of 21st-century justice, threatened to be the lasting image of the inquest.

But the jury’s decision to return such an intensely critical verdict suggests that the campaigners’ cries of whitewash were premature and inaccurate.

Inquest by numbers

100 Number of witnesses at inquest

41 Anonymous police witnesses

42 Days that court sat

28 Lawyers

7 Queen’s Counsel

11 Jurors

£6 million Total cost of inquest

£34,000 Estimated cost of lawyers’ sandwich lunches

Sources: Stockwell Inquest; the Brit Oval; Metropolitan Police Authority; Southwark Borough Council

Times Recommends

• How I lost the gift of joy for a while
• Why Ann Widdecombe has got it wrong
• Alas, it’s the end of the road for petrolheads