But the story of why the most handsome man in the Vatican became the Bishop of Cloyne has never been told before today.
For the first time, the high drama of ecclesiastical intrigue and ruthless church politics that has been kept under the wraps of pontifical secrecy can now be unveiled.
Twenty-three years after John Paul sent his celebrity choice to Cloyne, we witnessed this week how Pope Benedict XVI accepted with notable alacrity the resignation of the 73-year-old Bishop of Cloyne, whom his predecessor had acclaimed as a 'Jewel in the Vatican Crown'.
The timing of the resignation, coinciding with the paedophile cover-up scandals in Germany and America now engulfing the Pope, prompted the curt comment from the Holy See's spokesman, Fr Frederico Lombardi, that it was obvious why Magee had gone from Cloyne.
Remarkably, the Vatican was tight-lipped about the resignation of a prelate who was known to be "more Roman than the Romans", and who described himself as the "adopted son" of Paul VI.
Meanwhile, the Newry-born prelate, who was once tipped for promotion to Armagh and the coveted Primacy of All Ireland, has gone into hiding, now disgraced for recklessly failing to implement protection safeguards that put unsuspecting innocent children in schools and parishes to risk of violation by paedophile clerics.
The 'Good Shepherd' Magee, who had been sent to Cloyne by then Supreme Pastor John Paul II, has had his resignation swiftly accepted by the present 'Supreme Pastor', who is also being accused of the same negligence of children from rapist clerics that cost Magee his job.
Ironically, Magee, who is unique in Vatican history for being the personal secretary to three successive pontiffs, which made him privy to the Vatican's innermost secrets and provided him with a vast network of connections for his own advancement, has departed from the bishopric of Cloyne, which he had never sought or wanted.
Back in 1987, the Vatican's Congregation of Bishops and the then Cardinal Archbishop of Armagh, Tomas O Fiaich, had been searching for at least two years to find a new bishop to replace the aged John Ahearn, who was due to resign in 1986, on becoming 75.
Professor of moral theology at Maynooth, he was popular with the clergy and people of his native Cloyne.
However, in 1985, O Fiaich was also grappling with the question of who to back for the vacant presidency of Maynooth when he was confronted with a potentially dangerous scandal within the college that threatened to become public.
One of the college deans, Fr Gerald McGinnity, a priest of the Armagh archdiocese, reported complaints of students against the vice-president, Fr Michael Ledwith, relating to inappropriate sexual behaviour.
At private consultations in Maynooth, Armagh and Dublin with the Papal Nuncio Gaetano Alibrandi, a Sicilian, O Fiaich hit on the solution of naming McGinnity as the most-favoured candidate for Cloyne over O'Callaghan, while Ledwith would be next Maynooth president.
"It was a done deal," according to a witness of this private pact between the cardinal and the nuncio. "McGinnity was to be the next Bishop of Cloyne."
But this plan was thwarted in Rome, according to the well informed source who wishes to remain anonymous.
Pope John Paul II was increasingly unhappy with Magee, the source added.
In discussions with his Polish kitchen cabinet, John Paul II hit on the idea of bypassing McGinnity and adding Magee to the candidates' list, a selection which was rubber-stamped by the Congregation of Bishops -- to O Fiaich's horror.
On February 19, 1987, the Pope announced Magee's appointment to Cloyne and gave him the honour of ordaining him bishop on March 17, St Patrick's Day, in the Basilica of St John Lateran in Rome.
The source recalled how a change in Magee's personality occurred when he found himself-exiled from his beautiful villa inside the walls of the Vatican, close to the cobbled stones of the Santa Anna Gate, to the huge residence in Cobh, which was run-down, damp and in serious disrepair.
"The house was like a big shed standing in ruins," the source added.
The source claimed Magee was stuck in this big house, where the people and priests did not want him. This contrasted with the opulent life-style he had lived in Rome.
"In Rome, he lived the life of a prince," the source added.
"He was well-liked and was friendly to Irish visitors, offering them hospitality in his well-adorned villa with its underground church.
"He loved arranging audiences with the Holy Father for visitors. He was popular with young husbands and wives, many asking him to become the godfather of their children. He encouraged boys to nourish their vocation of becoming priests."
In Cloyne, Magee's personal deportment and manner of speech changed.
"He was in a wilderness. He became detached, aloof and authoritarian."
By 2009, Magee was misleading church and State that he was implementing nationally agreed child protection, which, as the report of the church's child protection body showed, he was not doing.
"It is ironic that Magee made it through the politics in Rome only to sink in a relatively rural Irish diocese," another source said.
"He really seems to have acted very stupidly or, perhaps, more arrogantly than stupidly.
"Was this because his Roman experience suggested to him that he was indestructible?"
Whatever the answer, Pope John Paul's decision to send Magee to Cloyne ended in shame.
After a year's sabbatical in Rome, McGinnity, the would-be bishop of Cloyne, found his Maynooth job gone. His academic career ruined. He was assigned to a parish in Co Louth by O Fiaich.
Later, McGinnity followed his conscience and blew the whistle on Ledwith, now an evangelist in America as the guru of a new-age cult.
But the key question in this story remains: why did Pope John Paul II become unhappy with Magee?
Magee may take that secret to his grave.
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