LIVE UPDATES: Pope Francis in the U.S.
The pope's plane touched down at JFK Airport at around 5:07 p.m. A crowd of 200 people cheered and waved hand-held Vatican flags as a smiling Pope Francis stepped off the plane.
Francis doffed his skullcap in the breeze as he made his way down the plane's stairs after flying in from Washington.
Cardinal Timothy Dolan of New York gave Francis a hug and a kiss as the pope stepped onto the tarmac, and Bishop Nicholas DiMarzo of Brooklyn greeted him with a warm handshake.
A high-school band played "New York, New York" as Francis made his way to the crowd, where Catholic schoolchildren were waiting to present him with a bouquet and a collection of prayers written by students in the city's 86 Catholic schools.
He handed out Mass cards, gave hugs and spoke with onlookers as people were taking cellphone photos of him.
Senator Charles Schumer got a chance to speak briefly to the pope as he greeted the crowd.
Pope Francis arrived in Manhattan by helicopter and hopped into a Fiat hatchback, traveling in the same modest style as he did in Washington.
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The military helicopter touched down at the Downtown Manhattan Heliport near Wall Street after a short flight from John F. Kennedy Airport.
The Fiat pulled up into Midtown and he climbed out of the Fiat and into his popemobile.
It slowly drove up Fifth Avenue surrounded by Secret Service agents as thousands of onlookers tried to get a glimpse of Pope Francis and snap a photo.
The pope waved and blessed the crowd as he smiled widely at the faithful.
When the motorcade concluded he arrived to a singing choir and a packed St. Patrick's to lead evening vespers.
Pope Francis kissed a crucifix and then blessed the cardinals around him. The processional made it's way down the center aisle. Once at the front of the cathedral, the pope stopped to bless a little girl in a wheelchair who cried tears of joy upon his touch.
Nuns in the pews erupted in applause when he thanked them for their service. Francis described religious sisters as "women of strength" and "fighters" who had a "spirit of courage" as they served at the forefront of the church. He said he wanted to offer "a big thank-you and to tell you that I love you very much."
The pope opened his visit to New York by expressing his solidarity with Muslims following a Mecca pilgrimage stampede in Saudi Arabia in which more than 700 people were killed. He offered a prayer for the victims from the St. Patrick's altar.
"In this moment of prayer, I unite myself with you all in prayer to God, our father, the all-powerful and merciful," he said.
The pope also raised the issue of the clergy sex-abuse crisis, by consoling clergy for the suffering the scandal had caused them.
Francis told members of religious orders and diocesan priests on Thursday that he was aware they had "suffered greatly" by having to "bear the shame" of clergy who had molested children. He thanked them for their faithful service to the church in the face of the scandal. He also made similar comments in Washington, DC.
The comments have angered advocates for victims, who say American bishops only took decisive action to stop perpetrators when lawsuits and government investigations revealed documents that showed the scope of the problem. The abuse crisis erupted in 2002 with the case of one pedophile priest in the Archdiocese of Boston, then spread across the country and overseas.
A Vatican spokesman defended the pope's remarks, saying it was appropriate to recognize the bishops' extensive reforms over more than a decade in response to the scandal.
Streets are blocked off around each of the pope's seven stops.
Crowds lined up hours in advance of the pope's arrival.
He'll celebrate Mass in Madison Square Garden Friday night. Earlier in the day he will visit the 9/11 Memorial and Museum and the United Nations.
Also among the pope's stops on Friday will be Our Lady Queen of Angels School in East Harlem.
The pope arrived in from Washington, which was the first stop on a whirlwind three-city U.S. tour that winds up in Philadelphia.
ABC7 News Anchor Ama Daetz is in Washington D.C. for the pope's canonization of Father Junipero Serra from California. Watch Ama's live coverage starting and join her as ABC7 News follows Pope Francis on this historic trip. Get her latest updates from Twitter and Facebook.
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The Associated Press contributed to this report.
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Written and produced by Ken Miguel