ISTANBUL, Turkey — If the Vatican had hired a high-profile New York public relations firm to help Pope Benedict XVI establish meaningful dialogue with Islam, continue along the path toward full communion with the Orthodox Church and move the world toward peace, it might have suggested a one-two punch: first Regensburg, then Turkey.

But things didn’t look so promising when my plane landed in Istanbul at the beginning of a week full of surprises.

Major street protests and diplomatic slaps by Turkish government officials threatened to overshadow the three objectives of the Pope’s visit: Confirm in the faith the tiny Catholic community in Turkey, build bridges of unity with the Orthodox Church and establish foundations for dialogue with Islam.

The populist protests and political cold shoulder were indicative of an underlying distrust within Muslim public opinion of all things “Benedictan.”

A taxi driver put it to me like this: “We are not going to kill him, but we don’t like him, and never will.”

But as Pope Benedict made his way throughout his four-day visit, threats gradually subsided, and the media, lacking compelling images of Muslim protesters, had no choice but to focus on his pastoral message.

In what turned out to be the smallest papal Mass on a foreign trip in recent history, Benedict celebrated Mass in Ephesus at the quaint stone cottage where the Blessed Virgin Mary is believed to have spent her last days, at the side of John the Apostle.

Pope Benedict gave them a message of hope and encouraged them to look to the example of Father Andrea Santoro, who was killed in Turkey earlier in the year. He was shot by a man who said he had acted in retaliation for Danish cartoons that had lampooned the prophet Muhammad.

As I write this article on the last day of the Pope’s visit, he is continuing to bolster the Catholic community in this predominantly Muslim community. He is having dinner with the Turkish Catholic Bishops’ Conference just a few floors below my room. His presence and his words, no doubt, are confirming them in the faith.

The millennium-old schism of the Orthodox Church has left a profound theological and cultural divide between Rome and Constantinople. Pope Benedict had no expectations to bridge the abyss in a four-day visit.

But he and Ecumenical Patriarch Bartholomew I reaffirmed their intention to seek full communion and they publicly reaffirmed that Christian division is a scandal.

In their common declaration after meeting in the Phanar, the see of the Ecumenical Patriarchate, they expressed shared sentiments and attitudes, but made no pretensions of resolving anytime soon the central issue of papal primacy.

“May our meeting be a sign and an encouragement to us to share the same sentiments and the same attitudes of fraternity, cooperation and communion in charity and truth,” said the declaration. “The Holy Spirit will help us to prepare the great day of the re-establishment of full unity, whenever and however God wills it.”

In press conferences and interviews, like the one I conducted with the head of the Greek Orthodox Archdiocese of America, representatives of the Orthodox communities focused most heavily on the importance of the Pope’s visit for the advancement of full rights for religious minorities in Turkey.

Under the secular Turkish state, no non-Muslim religious body has legal recognition. While proclaiming freedom of worship, the Turkish government has made life particularly difficult for the Orthodox by confiscating Church property and closing down their only seminary.

In a speech in the presence of Turkey’s religious affairs chief, Ali Bardakoglu, Pope Benedict launched a challenge for greater religious liberty in Turkey.

“Freedom of religion,” he said, “institutionally guaranteed and effectively respected in practice, both for individuals and communities, constitutes for all believers the necessary condition for their loyal contribution to the building up of society.”

The environment on the ground here was not favorable for rebuilding a relationship of trust between the leader of the Catholic Church and the Muslim world.

Even before Pope Benedict delivered his now infamous speech on Sept. 12 in Regensburg, the Turks were skeptical and perhaps afraid of Benedict’s ideas.

They knew that, as Cardinal Joseph Ratzinger, he opposed the entrance of Turkey into the European Union, pointing out the importance of preserving Europe’s geographical and cultural identity. In his mind, rather than looking for a European life preserver, Turks should close ranks and invest the successes of their secular state in bringing greater moderation and stability into a Middle East in despair.

But arriving in Turkey, Benedict offered an olive branch. The Turkish press splashed positive headlines about the Pope on all of its papers after Prime Minister Recep Tayyip Erdogan issued a statement saying the Pope had told him, “Turkey should take its place in Europe.”

Vatican spokesman, Jesuit Father Federico Lombardi, was quick to clarify. Father Lombardi said the Vatican does not have a political role in deciding on Turkey’s EU candidacy, but it does “view positively” the process of dialogue and drawing closer together that Turkey’s European Union aspirations represent.

That is a circular way of saying the Vatican will not oppose Turkey’s entrance, but it is a far cry from a pledge of full support. In fact, the “process of drawing together” may be understood as a reiteration of the Vatican’s well-known insistence that Turkey comply with the European Union’s values, especially the reciprocity of rights, full religious liberty, and proper and distinct roles of Church and state.

It was an old message with a different tone, but that was enough for the Turks. Tensions subsided and planned protests were canceled.

Some journalists have claimed Pope Benedict in Turkey flip-flopped on his Regensburg address. An attentive look, however, at the uncut versions of the Regensburg and Turkey addresses reveals remarkable similarities in content. To the international diplomatic corps in Turkey, for example, Pope Benedict once again insisted on the absolute rejection of violence in the name of religion.

“This assumes, of course, that religions do not seek to exercise direct political power, as that is not their province, and it also assumes that they utterly refuse to sanction recourse to violence as a legitimate expression of religion,” the Pope stated.

As in Regensburg, Benedict in Turkey did not contrast Christianity with Islam, but rather the peaceful harmony of faith and reason with those who try to separate the two, in particular, the imposters of religion who commit violence in God’s name.

Translated for modern Turks, the Pope’s message was that as human beings created by the one and true God, what we have in common is greater than what separates us. The foundation of universal human rights is our common and inherent dignity as people.

I’ve been on other papal trips, and the feel of this one was very different.

The throngs of well-wishers that generally welcome a pope, even in non-Catholic countries, were conspicuously absent. In their place were crowds of policemen and a Muslim population going about its business.

But the feeling I got was that it wasn’t business as usual. The good-hearted Turkish people were listening and reflecting on what this brave and sometimes controversial Pope had to say. They were comparing his words, now in an uncut form and in a more melodious tone, to their cultural and religious heritage.

They watch daily the slaughter of their Muslim brothers across their eastern border in Iraq and the political drama on all sides — in Syria, Iran, and Palestine. They are keenly aware of the threats by radical Islam and sectarian violence to their secular state, and they are looking for big and brave ideas.

And big ideas are precisely what Pope Benedict the Brave gave the Turks, Christians and Muslims alike.

Legionary Father Jonathan Morris is a commentator for the Fox News Channel and author of a popular blog: foxnews.com/fatherjonathan