As he walked from the former infirmary for sick and dying clerics, he knew his days as Bishop of Cloyne were numbered.
During an eight-hour emergency summit of the Irish Bishops' Conference held behind the centre's closed doors, the 72-year-old former secretary to three Popes had listened to colleagues' anger and frustration.
It was directed not only at his failure to apply commonly agreed child protection safeguards, but also for his having misled them that he was in full compliance with procedures.
In doing so, he had undone the slow progress made towards eradicating clerical sex abuse from the Irish Church. The meeting had been convened by a distressed Cardinal Sean Brady against a clamour of calls Dr Magee's resignation.
Since the controversy broke last year, Dr Magee resisted resigning and insisted, instead, that he was introducing the correct procedures and intended to oversee their full implementation in co-operation with the State inquiry, as well as carrying out his normal duties as Bishop of Cloyne.
However, Dr Magee's ego was dented when Archbishop Diarmuid Martin, of Dublin, and Bishop Willie Walsh, of Killaloe, publicly expressed their lack of confidence by inviting him to reflect on his position.
Just when Dr Magee appeared to be totally isolated, a lifeline was thrown to him by the support offered by Cardinal Brady, Archbishop Dermot Clifford, of Cashel, and Archbishop of Tuam, Michael Neary, who indicated that he should stay in office to correct his mistakes and co-operate with the State investigation.
Plunged
But the strength of the negative public and media reaction to the cardinal and the two archbishops plunged the Church into its biggest crisis since Brendan Comiskey stepped down in the diocese of Ferns.
Hence, the January 23 summit in Maynooth. In their statement at the end of that turbulent meeting, the bishops issued a reprimand to the beleaguered Dr Magee when they acknowledged that victims "have once again had their wounds of abuse opened by Church failure".
As one of the journalists kept outside in the dark and the cold, this passage struck me instantly as signalling Bishop Magee's doom.
The word "wounds" was exactly the one used by Pope Benedict in October 2006 when he personally called on the Irish Bishops to pursue the "urgent task to rebuild confidence and trust where these have been damaged".
We do not know the details of Dr Magee's consultations in the wake of the Maynooth summit.
What we do now know is that Dr Magee left Maynooth knowing his goose was cooked.
On Saturday, Pope Benedict divested him of his jurisdiction of Cloyne diocese.
John Magee now awaits his fate in the outcome of the State Investigation and possibly a Canon Law inquiry into his 'conduct unbecoming'.
The bell tolled for him on January 23, the Night of the Episcopal Long Knives.
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Sotto Voce
(Source: II)