McDonald had been in critical condition at North Shore University Hospital on Long Island since he suffered a heart attack last Friday.
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On the night of July 12, 1986, McDonald was on patrol in Central Park when he stopped to question three young boys.
After they ran away he found them, and one of the boys, 15-year-old Shavon Jones, pulled a gun and fired three times.
One bullet tore into the left side of McDonald's neck, followed quickly by another to his wrist and a third that lodged behind his right eye.
It was the first shot that splintered and pierced his spinal column, paralyzing him. Doctors told his wife Patti, who was three months pregnant, that he wouldn't live through the afternoon.
McDonald was paralyzed from the neck down and would use a ventilator for the rest of his life.
He is well-known for publicly forgiving Jones, who was later convicted of attempted murder.
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McDonald had continued as an active member of the police department despite the fact that he used a wheelchair and was only able to breathe with help from a respirator.
His death brought an outpouring of tributes. New York City Mayor Bill de Blasio said, ""There is no greater example of honor and service to others. Let it be our mission to continue his work."
Paralyzed NYPD Detective Steven McDonald dies
"Detective McDonald has been a unique source of inspiration and unrivaled pride to people the world over," said NYPD Commissioner James O'Neill in a statement. "A quadriplegic, he visited police station houses, schools, church groups and more, spreading his message of faith, forgiveness, and peace. No one could have predicted that Steven would touch so many people, in New York and around the world. Like so many cops, Steven joined the NYPD to make a difference in people's lives. And he accomplished that every day."
"Since that fateful day in 1986, Steven dedicated his life to fighting hate and encouraging forgiveness through his actions," said PBA President Patrick Lynch. "He was a powerful force for all that is good and is an inspiration to all of us. His, was a life well lived."
"Steven McDonald will always be a force for good and inspiration for good, in the NYPD and beyond," said former NYPD Commissioner Ray Kelly.
McDonald's passion was the New York Rangers, who established the Steven McDonald Extra Effort Award in 1988 for a player who goes above and beyond the call of duty both on and off the ice.
Every year he gave a Ranger the trophy and a check for $25,000 made out to the Steven McDonald Foundation.
The team tweeted a tribute to the detective:
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McDonald believed what happened was God's will, to turn him into a messenger of God's word. On March 1, 1987, he read a statement about his feelings toward the teenager who crippled him and said, "I forgive him."
In the years after the shooting, McDonald became one of the world's foremost pilgrims for peace. He took his message of forgiveness to Israel, Northern Ireland and Bosnia.
McDonald dreamed that Jones would join him on the speaking tours, creating an unlikely tag team with a mutual message of peace. But shortly after Jones' release from prison in 1995, he died in a motorcycle accident.
The McDonalds' son, Conor McDonald, joined the NYPD and became a sergeant last year. In 2007, Steven's wife Patti McDonald was elected mayor of Malverne, a quaint 1-square-mile suburban community of about 9,000 residents.
A wake will be held Wednesday and Thursday at St. Agnes Parish Center in Rockville Centre.
The funeral will be Friday morning at St. Patrick's Cathedral in Midtown Manhattan, to be celebrated by Cardinal Timothy Dolan.
(The Associated Press contributed to this report.)