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His father had entertained Edmund Campion at the ancestral home, Mount St. John, early in 1581. The family's Catholicism lapsed, but William, the youngest son, went abroad to train as a priest.
He was first at the seminary at Reims, then went to the Jesuits at Tournai (1582–1584). He would have joined the order, but his health broke down and forced him to keep at home for the next six or seven years.
In February, 1591, however, he was able to return once more to Reims, and, having been ordained, returned at midsummer 1592. Next May he fell into the hands of the English authorities (see Elizabethan Religious Settlement), and nine months later was executed at Tyburn. Harrington was tortured on the rack, hanged until not quite dead, then was subjected to disembowelment.
William's fate probably had an important literary side-effect. One of those who had sheltered him was Henry Donne, the brother of the poet John Donne. Henry was arrested, and died of the plague in Newgate Prison. John was a Catholic too, but later embraced the Church of England, eventually took Anglican orders and became Dean of St Paul's. What happened to William Harrington, and to John's brother Henry, may well have served to keep John Donne alive.
A posthumous detractor, Friswood or Fid Williams, an apostate Catholic, claimed that she had had a child by him before he was a priest. Fid also made many other accusations, both against him, and also against the rest of the clergy and the whole Catholic body.