He finds himself in an extraordinary position in Irish society.
First, newspaper headlines openly link him with lying. Even in our now-secular society, this is unprecedented given the still-important position of the Catholic Church, not to mention our harsh libel laws.
Isolated
Second, he has been isolated by his fellow bishops. Archbishop Diarmuid Martin and Bishop Willie Walsh may not have called on him to resign, in so many words.
But there is no doubt that to be asked by fellow bishops to consider his position and to act in the best interests of children is the same as being asked to go.
Third, a Government minister, Barry Andrews, has asked him to consider his position which, again, is tantamount to asking him to resign.
But, who is John Magee and how is it possible to arrive at this unprecedented level of isolation?
How could a man who was a Vatican insider for many years have slipped so badly in the esteem of fellow bishops and of the State?
Magee, born in Newry in 1936, knows the corridors of the Vatican better than most priests or bishops.
Ordained for St Patrick's Missionary Society, he was a private secretary to Pope Paul VI and later to the short-lived John Paul I.
He was reported to have found the Pope dead in bed in 1978.
He continued as a private secretary to Pope John Paul II, who made him Master of Ceremonies.
Nearly 20 years ago, in 1987, he was appointed Bishop of Cloyne.
He may know the Vatican but it cannot be said that Bishop Magee has inspired any affection in the Irish public.
He has been remote in his relationship with that public by comparison with fellow bishops, such as Willie Walsh and Diarmuid Martin.
He has been involved in modernising the Catholic boy scouts movement and has shown an interest in encouraging both lay men and women to become involved in the church.
His most high-profile involvement in recent years concerned a controversy over his plans to make changes to the interior of Cobh Cathedral.
The plans were opposed by an effective and determined conservationist group locally.
Ultimately An Bord Pleanala turned down his application.
This, again, was significant.
That he got into this fight with Catholics in Cobh in the first place suggests that his years in the Vatican taught him little about how to deal with affairs in the 21st century.
In some ways, he is completely out of his time.
His failure to fully implement child protection guidelines is entirely in line with the behaviour of the Church in the 1980s.
So is his capacity for saying things which turn out not to mean what most of us think they mean.
In November 2005 he told the then Minister for Children, Brian Lenihan, that Church guidelines were "fully in place and being fully complied with" and that his diocese was also compliant with Government guidelines.
This turned out not to be true, as far as the present minister, Barry Andrews, is concerned.
Deception
In 2007, his diocese told the HSE that it worked in compliance with Church and statutory guidelines.
This too, Barry Andrews pointed out, was not the case.
The diocese was handling a child abuse case which it had not told the HSE about.
In Barry Andrews, Magee has met a minister -- not even a full member of the Cabinet -- who is willing to go head to head with him on this issue.
The decision to have Judge Yvonne Murphy's Dublin Archdiocese Commission of Investigation examine the situation in Cloyne is evidence of this.
So far, Magee has resisted calls, both clear and implied, for his resignation.
The fact is, it may not really matter whether he stays or goes.
His authority has vanished.
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Sotto Voce
(Source: EH)