The Pope in Jerusalem
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AP
Pope Francis and President Shimon Peres. Photo by AP

Pope Francis said goodbye to Israel Monday evening after an historic three-day visit to the holy land, leaving behind newly earned fans as well as politicians amazed at his unprecedented invitation for a peace prayer summit in Rome.

A church delegation in long black robes and fuchsia sashes arrived at Ben Gurion Airport, lining the red carpet to help accompany the pope to the El Al plane awaiting him. Both President Shimon Peres and Prime Minister Benjamin Netanyahu met him on the runway and accompanied him to the stairs of the plane. A military honor guard and musicians accompanied the pope with honors usually reserved for heads of state.

After being surrounded by a sea of black - both officials and clergymen - the man in white ascended the steps, turned around, and waved goodbye.

The pope, who began his journey on Saturday in Jordan, arrived Sunday in in the West City of Bethlehem where he met with Palestinian President Mahmoud Abbas, attended Mass at the Church of the Nativity and made a surprise stop at the West Bank separation barrier. Later in the day, he landed Israel's Ben-Gurion Airport where he was greeted by Prime Minister Benjamin Netanyahu and President Shimon Peres.

The pope began his day in Jerusalem with a visit to the Temple Mount, after which he visited the Western Wall. Pope Francis than laid a wreath at Mount Herzl and visited Yad Vashem. He also met with Peres and then with Netanyahu. He will conclude his day in Jerusalem with visits to various Christian sites including the Church of Gethsemane and High Mass in the Room of the Cenacle.

8:52 P.M. Latin Archbishop Fouad Tuwal, who saw the pontiff off at the airport, said he was pleased that the trip had gone so well. Given a recent rash of hate crimes (so-called 'price tag' attacks), including some aimed at Christians, there were fears that extremists could try to disrupt the trip.

"It's such a small minority who do such radical things - they are not part of normal life. Thank God, the trip ended well, without any problems, without any attempts at anything negative to spoil the pope's important visit it," Tuwal, who is originally from Jordan, told Haaretz with visible relief.

8:04 P.M. The pope, climbing up the steps to the El Al plane, turns around, and waves goodbye.

7:55 P.M. Pope arrives at Ben Gurion Airport.

5:20 P.M. Holy Mass with the Ordinaries of the Holy Land and the Papal Suite in the Room of the Cenacle in Jerusalem.

4:00 P.M. Pope meets with priests, men and women religious and seminarians in the Church of Gethsemane at the foot of the Mount of Olives.

3:30 P.M. Pope holds private meeting with the Ecumenical Patriarch of Constantinople Bartholomew I at the building next to the Orthodox church of Viri Galileai on the Mount of Olives.

2:10 P.M. Netanyahu tells Pope Francis he is looking forward to day when terrorism is over and the separation barrier is not needed.

2:00 P.M. In a speech at the President's Residence the pope says he prays for the State of Israel and for peace.

"Mr. President, I vow to pray for the institutions of the State of Israel and for its citizens. I especially promise to continually ask God for peace and for the blessings related directly to peace: security, prosperity and fraternity," he says.

"We unequivocally reject everything opposed peace and coexistence between Jews, Christians, and Muslims including: Violence and terrorism and all forms of discrimination based on race or religion; all forms of anti-Semitism; acts of intolerance toward people or place or worship of Jews, Christians and Muslims.

"Various Christian communities live in Israel. They are an inseparable part of the society and they are engaged in it civically, politically and culturally. Christians wish to make a contribution unique to their identity for the good of all and for the achievement of peace, as equal citizens that reject all extremism. Their presence and the recognition of their rights constitute a guarantee for healthy diversity and proof of the existence of democratic values and their anchoring in the conduct and essence of the state."

Peres and Francis at the President's Residence (Yosef Avi Yair Engel)

1:24 P.M. Peres formally accepts Pope Francis' invitation for a joint prayer session with Palestinian President Mahmoud Abbas at the Vatican.

"I will be happy to accept ... your generous invitation," says Peres, describing Francis as a "moral authority."

"Your call for peace will sound a positive echo throughout the region," Peres says.

"We will work together, Jews, Christians and Muslims to bring an end to the conflicts," Peres says speaking alongside the pope, a choir of children standing behind them.

1:00 P.M. The Prime Minister's Office says Netanyahu explained to Francis Israel's rationale for building the wall while they were at the terrorism memorial. Netanyahu asked Francis to add the memorial in at the last minute, and showed him the section dedicated to the victims of the 1994 bombing of a Jewish association in Buenos Aires that killed 85 people. The Argentinian-born Francis was an auxiliary bishop of Buenos Aires at the time of the attack and later became archbishop.

"I explained to the pope that constructing the fence (separation barrier) prevented many more victims of Palestinian terror, which continues today," Netanyahu said.

12:40 P.M. Pope Francis meets with President Shimon Peres at his official Jerusalem residence, calling the veteran politician and Nobel Peace Prize laureate a "good and wise man."

"With my fantasy and my imagination I would like to invent a new blessing," the pontiff says in unprepared remarks. "Blessed is the man who enter this house of a good and wise man."

12:05 P.M. In a parley with the Sephardi Chief Rabbi, Shlomo Amar, and Ashkenazi Chief Rabbi, David Lau, Francis calls for Jewish-Christian friendship, calling the progress made in recent decades between Jews and Catholics "a genuine gift of God."

Francis with the Sephardi and Ashkenazi chief rabbis (AFP)

11:30 A.M. The Western Wall rabbi says he gave Francis a map of the area dating back 1,400 years. "The one who created this map wrote the words 'Soloman's Tabernacle' on the Temple Mount," the rabbi says. "There may be other things on the [Temple Mount] now but it's still the holiest place for Jews."

11:00 A.M. Pope Francis leaves an inscription in the guest book at Yad Vashem: “With shame for what man, who was created in the image of God, was able to do. With shame for the fact that man made himself the owner of evil. With shame that man made himself into God and sacrified his brothers. Never again, never again.” The inscription is signed simply “Francisco” and the date.

10:30 A.M. At the Yad Vashem Holocaust memorial, Francis prays before a crypt with ashes of victims and lays a wreath of yellow and white flowers in the "Hall of Remembrance.

Pope Francis observes a moment of silence after laying a wreath during a ceremony in the Hall of Remembrance at the Yad Vashem Holocaust memorial. (Reuters)

And then one by one, he kisses the hands of a half-dozen Holocaust survivors as he hears their stories and of loved ones killed by the Nazis during World War II.

"In this place, this memorial of the Shoah, we hear God's question echo once more: 'Adam, where are you?'" Francis says at Yad Vashem quoting from Gen 3:9.

"Here, before the boundless tragedy of the Holocaust, That cry – 'Where are you?' – echoes like a faint voice in an unfathomable abyss."

"A great evil has befallen us, such as never happened under the heavens. Now, Lord, hear our prayer, hear our plea, save us in your mercy. Save us from this horror."

"Grant us the grace to be ashamed of what men have done, to be ashamed of this massive idolatry, of having despised and destroyed our own flesh which you formed from the earth, to which you gave life with you own breath of life. Never again, Lord, never again!"

9:45 A.M. Deviating from his packed schedule, Francis visits a memorial to Israeli victims of terrorism before traveling to the Yad Vashem Holocaust memorial.

9:30 A.M. The pontiff arrives at Mount Herzl to to lay a wreath at the grave of Zionist visionary Theodor Herzl.

Netanyahu and Peres accompany Pope Francis on his surprise stop at a memorial to Israeli victims of terrorism. (Avi Ohayon/GPO)

9:10 A.M. Pope Francis prays at the Western Wall. He places his hand on the ancient stones and puts a note with the text of the "Our Father" prayer written in his native Spanish in one of the cracks between the stones.

Leaving the Western Wall, Francis writes in Kotel guest book,"I came to learn from the older brothers the significance of the place. I came to pray for peace all over the world."

Pope Francis touches the stones of the Western Wall, Judaism's holiest prayer site, in Jerusalem's Old City May 26, 2014 (Reuters)

 Pope Francis walks with religious leaders near the Western Wall in Jerusalem's Old City on May 26, 2014. (AFP)

8:30 A.M. The pope enters the Dome of the Rock, the iconic shrine located at the third-holiest spot in Islam.

Pope Francis stands in front of the Dome of the Rock during his visit to the Temple Mount in Jerusalem's Old City, May 26, 2014. (Reuters)

8:15 A.M. Pope Francis urges non-violence in a meeting with the Grand Mufti of Jerusalem, Sheikh Mohammad Hussein.