When news came last week that Cardinal Keith O'Brien was being exiled from Scotland for "prayer and penance", memories came flooding back to Lenny, the former priest who has accused O'Brien of inappropriate behaviour.

He remembered being a young priest in the 90s and telling O'Brien, then an archbishop, that he could not pledge allegiance to him and was leaving. The cold chill of O'Brien's disapproval followed him down the path of the archbishop's official residence and seeped into him in the dole office where he queued for benefits.

Years later, the two were forced to meet again. O'Brien was a cardinal. Lenny reminded him of an unfortunate prank O'Brien had organised when he was spiritual director at Lenny's seminary. Ah, the cardinal admitted, other staff had later chastised him for bad judgment. "But these days," he smiled, "I can do what I like."

In February, O'Brien resigned after complaints of sexual misconduct, not just from Lenny but from three serving priests in his own diocese. His statement admitted inappropriate conduct "as a priest, archbishop and cardinal", a clear indication that his sexual choices had been a lifestyle and not isolated indiscretions. Three months on, there has been no official Vatican investigation and is no prospect of one. Some interpreted last week's statement of O'Brien's exile as Vatican "action". To the four complainants, it was another smokescreen. So what has really been going on for the last three months, behind the scenes of the Catholic church?

The trigger for the four complainants going public was not, as some suggested, the resignation of Pope Benedict and the ensuing papal conclave. Their statements were with the nuncio on 8 February. Benedict resigned on the 11th. It was, instead, a message from the nuncio, via an intermediary, that the cardinal would retire to a life of "prayer and seclusion". It was "Vatican-speak". The complainants knew that everything was about to be swept under the clerical carpet. Last week's statement was uncannily familiar. The cardinal would undergo "a period of prayer and penance". But if the Vatican really wanted that, why had they not insisted on it immediately? Clearly, it wasn't his sexual misconduct that triggered this statement. So what was it?

Key concepts govern Catholic church behaviour: authority, obedience, cover-up, secrecy and clericalism. Clericalism is about deference, a demand for respect without scrutiny.

These traits have been seen often in church history. The protection of the institution rather than victims in abuse cases. The movement of paedophile priests from parish to parish in an "out of sight, out of mind" policy. The astonishing admission by the Scottish church that the child abuse audits it promised back in 1996 had not been carried out. There is a reason why the Catholic church is weak in processes and procedures, why things are "fixed" in dusty corners. The hierarchy demands authority, without offering accountability.

After the cardinal resigned, church secrecy created a vacuum. The nuncio's office refused to give information about any investigation. "Not even whether it exists," the Observer was told.

The four had to break the silence by battering individually on the Vatican's doors. Lenny even phoned Rome, asking to speak to Cardinal Ouellet, head of the Congregation for Bishops, who would be expected to investigate any matters relating to cardinals. "You think I can speak on the phone?" demanded Ouellet. "I don't think so." Well, write to me, said Lenny. Ouellet wrote a perfunctory letter. His department was considering Lenny's testimony "very carefully". But in future, please contact the nuncio. To this day, the formal statements of the four have been met only with offers of informal "chats".

Media stories became inaccurate and contradictory. There was an investigation. There wasn't an investigation. (There wasn't – at least not a meaningful one.) Bishops' appointments were on hold. (They weren't – they just couldn't be filled.) Where was the cardinal through all this? A letter sent by O'Brien shortly after he resigned had a Scottish postmark. Then he turned up in a church property in Dunbar, where he had been due to retire and where his close friend, John Creanor, is parish priest. His appearance became public, courtesy of the Sun.

It was an obvious set-up. O'Brien was photographed moving in and gave a brief interview. The drip, drip of stories became a flow. The Catholic media office was supposedly furious – and largely unavailable for official comment. The director of communications, Peter Kearney, said only Rome could handle this. Nobody in Scotland had authority to challenge a cardinal. When O'Brien resigned, archbishop Philip Tartaglia was appointed temporary leader of St Andrews and Edinburgh. But Tartaglia failed to confront the issue, and behind the scenes those "church insiders" were critical. "He is completely lacking in leadership qualities," one told me. Last week Peter Kearney told the Observer there could be no Scottish investigation because the nuncio had – rightly – not divulged the names of the complainants. But the nuncio had. What Kearney didn't know, apparently, was that Joseph Toal, bishop of Argyll and the Isles, had been given names and asked to be a contact point.

It was into this chaotic scrum that last week's Vatican statement was lobbed. O'Brien's cardinal sin was obvious. Not sexual misconduct. Being visible. The four hardly cared if he was in Scotland. "He's got to live somewhere," one told me. What they wanted was an official investigation.

There were several ironies. Firstly, O'Brien had been painted as the elderly repentant gent who just wants "a quiet retirement". In fact, he is still Britain's most senior Catholic. His power is such that nobody would challenge him – and let's not forget that abusing power led to his downfall.But this is no longer about personal failure. It's about systemic failure. "As a church, we have failed to come to terms with homosexuality," says Professor Werner Jeanrond, a Catholic theologian who held the chair of divinity at Glasgow University, before becoming the first layman to run the Benedictine hall, St Benet's, at Oxford University. "The highest clerical representative of the church is himself a victim of the system which didn't allow him to own his homosexuality."

But O'Brien is not the main victim in this. If people knew what the four's statements contained, they might not dismiss the accusations so readily and call for easy forgiveness. This is not about vengeance. It's about transparency and an end to clericalism. "You cannot forgive," Jeanrond points out, "if you do not know what is to be forgiven."

O'Brien is a timebomb. Anyone who thinks this is only about his behaviour – or just the behaviour of Scottish clergy – is naive. It is about clergy worldwide. But the scandals behind at least one other Scottish bishop are legendary. Sexual "misconduct" is rife among the priesthood. Heavy drinking is common. Payoffs have been made to cover scandals. Serious abuse has been concealed. O'Brien knows where the bodies lie. And the hierarchy knows he knows.

But he is not the only timebomb. While writing this, an email arrived from one of the priests. He had been called to a dying woman's house. She would die before midnight, he thought. But this family he met had hope. The word hope was touching. It put everything in context. Perhaps, said the priest, Pope Francis represented hope. Perhaps he would instigate an investigation. And if not? Well, despite what the cardinal once thought, no person or institution is untouchable. Those who know what those four statements contain know they include information that could blow this scandal even higher. That is not a threat. More, a prophetic warning.