The resignation of Martin Callinan as Garda Commissioner and the very full apology from Alan Shatter in the Dáil on Tuesday may have eased the pressure on the Government this week, but it is still caught in the midst of a Category 5 political storm.

Despite the dramatic events of the past few days, there are still a number of irritants, puzzles and questions for which there has yet been no satisfactory answer. The information being released has been strictly controlled and limited.

Question 1: Was Martin Callinan effectively sacked?

Taoiseach Enda Kenny took huge exception to Micheál Martin's suggestion that this was the case in the Dáil yesterday, claiming he was being accused of being a liar by the Fianna Fáil leader. So what happened?

When the import became clear of the practice of Garda divisional headquarters routinely recording telephone calls, the Taoiseach dispatched a senior civil servant to go to Callinan's home on Monday evening, the night before the Garda chief stepped down. It was thought the person might have been the top official in the Department of An Taoiseach, Martin Fraser, but Kenny disclosed yesterday that it was Brian Purcell, the secretary general of the Department of Justice.

The Government said Purcell was instructed to talk to Callinan about the response to the unfolding situation. But, crucially, the Taoiseach and those close to him say he was also told to impress upon Callinan how “serious” and how “grave” the situation was.

Was this tantamount to saying, “No pressure, but here’s your P45”, as the opposition has claimed? Certainly, it has been suggested that Callinan was told firstly by Purcell that he might not survive the Cabinet meeting. Then the following morning, in a further conversation, he was told the situation had got worse. Several Ministers also believe, though not privy to the process, that there may have been a political imperative for Callinan to go.

When crises such as this one erupt, it is almost as if the political Gods demand it will not be resolved unless there is a head on a plate. Was this the case? Although the Taoiseach fiercely contested the assertion, to many it looks as if Callinan was effectively forced from his position. We won’t know unless there is a willingness to share what was said in the conversation with Brian Purcell.

Question 2: Is Alan Shatter safe?

Yes, but only for the moment. Shatter is now only one crisis short of walking the plank. If the current controversy is examined, he cannot really be seen as blameworthy. But it comes on top of a raft of crises in which he has been a central protagonist. His lack of knowledge also dents the slightly hubristic claim made on his behalf of the 6am starts at work, and his extraordinary, encyclopaedic command of everything that moves within his department.

The facts in this matter do tend to support him though. The Garda Síochána Ombudsman Commission (Gsoc) sought to rely on recordings of telephone calls it had obtained from the Garda Síochána in a prosecution of four gardaí over the assault of a man in Waterford. It was only when the evidence was ruled by the judge to be inadmissable that Gsoc raised a flag about the propriety of using such recordings.

It appeared almost as a coda and specified only Waterford Garda station, and did not suggest the practice was widespread.

In addition, the report was not sent directly to the department or the Minister, but posted on Gsoc’s website. The possible ramifications were missed by everybody - Gsoc, journalists and the department. But not seemingly - and ironically - the Garda Síochána, which acted on foot of the report. There is a valid argument that the department should look more closely at issues like this in which it is an obvious interested party.

The two-week delay in informing Shatter of Callinan’s letter of March 10th was also a serious lapse of judgment within the Department of Justice. There were some extenuating circumstances, including a bereavement, but it is clear the Minister should have been informed in a manner other than the slipshod way it happened on Monday evening.

Question 3: What did the Attorney General Maire Whelan know, and when?

This is an area which is surrounded by a thick fog. We do know the Garda Síochána contacted her office on November 11th last year to alert her to the practice of routinely recording phone conversations in Garda stations throughout the country. We do know that on foot of the contact, the practice of routine recording was stopped in November.

We also know Callinan set up a working group within the Garda to ascertain the extent of the recording and for how long it had been in place. It also began to collected the recordings and transcripts that had been stored over the years.

Shatter said yesterday that the Attorney General was aware in November that recording took place and that she knew of the existence of tapes (and the possible existence of other tapes). The Government's response is that the information supplied to her was "tentative", or as Minister for Public Reform Brendan Howlin put it, there were no "red flags flashing".

It is clear that the culmination of the discovery order process in the civil proceedings being brought by Ian Bailey crystallised thinking in relation to the gravity of the recording. But the question remains: why was this only brought to the attention of the Taoiseach last weekend?

If no flags had been raised in November, should there have been? Was the information supplied by the Garda Síochána inadequate in that it underplayed a practice that should have been alerted to Cabinet? Was there an imperative for anybody dealing with the case in February and early March to alert the Taoiseach of the seriousness of the situation?

Question 4: What is the background to the chair of the Commission of Investiga tion and the terms of reference?

No details have emerged about either. And no indication has been given as to the thinking as to how the commission might operate.

The Government is indicating it will be early April before the terms are published, and it is likely the identity of the chair will not be known until then. It seems the decision to establish the commission was taken “on the fly” in Cabinet.

The most senior figures in Government may have been privy to some more information and been given an indication as to the contents of some of the recordings - and there is always the possibility that some contained privileged communications between solicitors and their clients. There is also the issue that such recordings which should have been made available to court proceedings were withheld.

There will be a need to establish when the practice first started, and which government authorised it. While originally intended for 999 calls, and to investigate bomb threats and coded passwords from paramilitary organisations, how did the practice expand to include routine calls coming in and out of divisional headquarters? Were there specific lines that were chosen or were all lines subject to recording? How extensive was the practice and how routine was it? Were all recordings retained? Is there evidence of recording being used for nefarious purposes such as eavesdropping or clandestine evidence-gathering?

Also, under what authority did the practice continue? Were there rules or codes, or was it done on an ad hoc or “inherited practice” basis? At what stage did the Garda Síochána begin to question the validity and legality of the practice? Were the recordings used in the context of any other criminal case or prosecution? Was the query about the practice submitted to the Attorney General’s office prompted by the Waterford investigation or by the discovery process in the case being brought by Ian Bailey?