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Father Judge hurried to the World Trade Center and was met by his close friend Mayor Rudolph Giuliani, who asked him to pray for the victims, New York, and the first responder’s safety. At 9:59 AM the South Tower collapsed and debris crashed through the North Tower lobby where Judge was offering aid and comfort. He was hit in the head and killed while giving the last rites to a victim.
The act of his body being carried out soon after to St Peter's Church was captured in the film 9/11, and a photo appeared in a report from Reuters. It became an iconic image regarding 9/11. Mychal Judge’s body occupied body bag #0001, and was certified the first fatality because his was the first body to be recovered and taken to the coroner.
Father Judge's funeral was attended by over 3000 people on September 15, 2001 at St Francis of Assisi Church in Manhattan. At the funeral, President Bill Clinton said that Judge's death was "a special loss. We should lift his life up as an example of what has to prevail ... We have to be more like Father Mike than the people who killed him"
The Légion d'honneur was awarded to him by France. Father Judge's fire helmet was presented to Pope John Paul II. Several members of the U.S. Congress nominated him for the Congressional Gold Medal as well as for the Presidential Medal of Freedom. In 2002, the City of New York renamed part of W. 31st Street "Father Mychal F. Judge Street."
Many within the Roman Catholic Church have called for sainthood for Father Mychal Judge. Several churches independent of Rome including the Orthodox Catholic Church of America have declared him a saint despite resistance from the Holy Father. Father Judge is seen as a de facto saint by widespread acclamation of the faithful, as was the custom of the early Church.
Following his death a few of his friends and associates revealed that Father Mychal Judge was gay as a matter of orientation rather than practice, as he was a celibate priest. According to fire commissioner Thomas Von Essen: "I actually knew about his homosexuality when I was in the Uniformed Firefighters Association. I kept the secret, but then he told me when I became commissioner five years ago. He and I often laughed about it, because we knew how difficult it would have been for the other firemen to accept it as easily as I had. I just thought he was a phenomenal, warm, sincere man, and the fact that he was gay just had nothing to do with anything."
In his honor, Congress passed The Mychal Judge Police and Fire Chaplains Public Safety Officers Benefit Act into law in 2002. This was the first time the federal government ever extended equal benefits for same-sex couples, allowing the domestic partners of public safety officers killed in the line of duty to collect their federal death benefit.
Judge was a long-term member of Dignity, a Catholic LGBT activist organization that advocates for change in the Catholic Church's teaching on homosexuality. On October 1, 1986, the Vatican's Congregation for the Doctrine of the Faith issued an encyclical, On the Pastoral Care of Homosexual Persons, which declared homosexuality to be a "strong tendency ordered toward an intrinsic moral evil". In response, many bishops, including John Cardinal O'Connor, banned Dignity from diocesan churches under their control. Father Judge then welcomed Dignity's AIDS ministry to the Church of Saint Francis of Assisi, which is under the control of the Franciscan friars, thereby partially circumventing the cardinal's ban of Dignity.
Judge disagreed with official Roman Catholic teaching regarding homosexuality, though by all accounts he remained celibate. Judge often asked, "Is there so much love in the world that we can afford to discriminate against any kind of love?"
Despite all the evidence above and much more, many Christian evangelicals still claim the father wasn’t gay and assert it is a plot to make him a homosexual icon and slander the name of a saint.