At almost 5pm Cairo local time (3pm GMT), Egypt's President Abdel-Fattah El-Sisi showed Pope Francis to the Alitalia plane that would fly him back to the Vatican, bidding him farewell after a 27-hour visit rightly described as historic.

Pope Francis had arrived to Egypt Friday afternoon and was received by Prime Minister Sherif Ismail. Pope Francis visited the presidential palace, the headquarters of Al-Azhar, the Coptic Orthodox Cathedral and St Leo’s Patriarchal Seminary in Maadi during the time of his stay.

On each of these stops, as in a gathering with public figures to a luncheon hosted by President El-Sisi, Pope Francis made statements calling for tolerance, peace and an end to violence. He also offered a homily at a mass he led, with joint Coptic and Catholic prayers, at the Air Defence Stadium in Cairo.

The Pope's message was clear: one of love and acceptance of the other, respect of freedoms and human rights, and combating selfishness and all forms of tyranny.

“We should avoid the temptation of being a pharaoh,” Pope Francis said in his address to priests and seminarians who gathered at St Leo’s Patriarchal Seminary in Maadi Saturday afternoon – the last stop for the Pope before he left Egypt.

In a split second, the Pope smiled and laughed, saying jokingly, “But we are in Egypt.”

The Pope was addressing his audience on the things a good priest or seminarian should avoid as they “turn difficulties into opportunities and lead the masses towards the river of love.”

Earlier in the day, Pope Francis, during his homily, had prayed for the “courage of forgiveness and the courage of helping those who fall.”

Beyond his call for love and warning against tyranny, Pope Francis remind audiences at each stop that civilisaiton is the making of those who call for peace, respect the dignity of the human being, pursue development and refrain from acts of injustice, which he said, “are not forgiven by history.”

Pope Francis and President El-Sisi had already held a meeting at the presidential palace following an official reception head of the executive accorded the visiting head of the Vatican Friday afternoon.

The meeting, according to one source close the papal delegation, was “very courteous and very civil, of course".

During his meeting with El-Sisi, Pope Francis expressed his sympathy with the loss of lives of Egyptian Copts during attacks by the Islamic State group and was reassured by the clear language of the Egyptian president on the state’s commitment to protect all its citizens, including Copts, and to secure their freedom of faith and freedom of worship, “despite some issues that President El-Sisi did say still require sensitive treatment.”

An Egyptian government source said that the encounter of the Pope and the president was cordial and very friendly. 

The Pope, also did bring up during the visit, according to a source close to the papal delegation  the concern and the pain of the family of Guilio Regeni.”Regeni, an Italian researcher, was found dead — "brutally killed" according to his family — in February 2016 a few days after disappearing.

During his statement before the closing session of the international conference on peace at the headquarters of Al-Azhar, Pope Francis underlined the need to respect the religious rights and freedoms of the other and to pursue the call of tolerance in fully awareness that no act of violence can be committed in the name of God.

It was the meeting of Pope Francis with Pope Tawdros, the Coptic patriarch, at the Coptic Orthodox Cathedral that illicited the closest attention of Egyptian Christians. Copts are said to number 8-10 million, and Catholics around a quarter of a million.

The historic signing of an agreement to jointly recognise the baptism of Christians by both churches offered good news to Egyptian Christians who were pleased at the rapprochement between the leading churches.

Following the signing of the agreement, Pope Francis and Pope Tawdros led joint ecumenical prayers at St Peter and St Paul Church, that was subject to an Islamic State group terror attack that killed over 30 people in December.

Both Pope Francis and Pope Tawdros lit candles in memory of the victims.

Pope Francis also paid tribute to the souls of over 50 victims who killed by another Islamic State group attack that hit two Coptic churches in Tanta and Alexandria during Palm Sunday prayers.

The visit of Pope Francis to Egypt is the first of the head of the Vatican since 2000 when Pope John Paul II visited.

The visit was conducted under very strict security scrutiny, especially in Heliopolis, the venue of the airport and the presidential palace, and Zamalek, the residence of the ambassador of the Vatican, where the Pope stayed during his 27-hour visit.