Two images, both unexpected, dominated the year for Pope Benedict XVI.

The first was iconic in a malevolent sense, with fanatical Muslims burning him in effigy after his Regensburg lecture. The second was iconic and irenic: the Holy Father praying in the Blue Mosque of Istanbul.

The papal year began with the release of the encyclical Deus Caritas Est (God Is Love ) and much of what happened afterward would test the limits of papal charity.

The Holy Father’s decision, only a few months after his election, to request a special meeting with Muslim leaders in Cologne already signaled that he considered Christian-Muslim relations, especially in Europe, to be an issue in need of significant attention.

That meeting was full of warm exchanges and respect, a notable achievement in a Europe where there are often social tensions with the large Muslim minorities in Germany, France, Holland, Belgium and Britain.

Those tensions dominated the early part of 2006, when the Danish cartoon controversy erupted, with Muslim mobs throughout the world resorting to violence to protest caricatures of the prophet Muhammad.

No doubt the Holy Father took note as governments and newspapers across Europe and North America — including influential Vatican voices — rushed to placate the inflamed Muslims in the streets. And no doubt the controversy pointed to potential difficulties ahead for his November trip to Turkey; in Trabzon, an Italian priest, Father Andrea Santoro, was murdered by an Islamic radical upset about the Danish cartoons.

Against this background, with his usual careful preparation, the Holy Father returned to Germany in September and addressed himself at Regensburg to a dominant theme of his entire theological career, namely that reason and faith are both necessary to know the truth.

And then he addressed head-on a central question of our time: Is it reasonable to commit violence in the name of faith? He said No, and asked whether contemporary Islam could give as emphatic a rejection of violence.

It is a question oft-discussed but never formally raised in polite circles. The settled routine after an Islamist terrorist act is for the president/prime minister/Prince of Wales to rush to a mosque to proclaim Islam a religion of peace. Benedict was bold enough to ask the question that has been discussed at kitchen tables the world over since 9/11: Is there something in contemporary Islamic thought that encourages such violence?

Benedict does not raise questions to indulge idle curiosity.

The theologian in him asks questions because he thinks good questions can lead to good answers. His own, implied, answer to the question of Islam and violence is that there are bad religious ideas afoot in the Islamic world — as has also been the case at times in Christian history — that do justify violence, and therefore need to be answered by good religious ideas.

The central geopolitical question of the post-9/11 period is how to counter the malevolence of Islamist terror.

Benedict thinks that is also a spiritual question.

One option is to propose democracy and economic liberty in the Islamic world; another is to propose secularism to reduce religious extremism. Benedict understands better than anyone that bad religious ideas cannot be overcome by non-religious ideas or even worse, anti-religious ideas. Bad religious ideas need to be confronted by good religious ideas, which is simply to say that religious errors need to be corrected by religious truths, not political non-sequiturs or anti-religious errors.

This was why he raised the whole matter in Regensburg, and did not shy away from the same themes in Turkey.

The tone was different, but Benedict did not pretend to overlook the Turkish denial of religious liberty, and he mentioned the murdered Father Santoro by name. What Turkey added was something left implicit at Regensburg, which was that Islamic history itself contains the answer to the temptation of violence, and it is for Muslims themselves to rediscover that heritage in order to confront the challenges of the present day.

Turkey’s own history boasts periods of peace and prosperity under Islamic rule, with ample space given to religious minorities to live in harmony.

That was captured by the moment of prayer in the Blue Mosque. Silent prayer is the antithesis of violence, and it is something shared by Christians and Muslims alike. That it created such a stir — was the Pope capitulating to the Mohammedans, asked some — indicated how off-track the discussion had wandered. The Pope was praying, alongside Muslims, and Muslims who can pray alongside Christians might serve to dissuade their fellow believers from blowing them up.

In retrospect, 2006 was the year in which the Holy Father asked difficult questions in a lecture hall, and he prayed in a place dedicated to prayer.

That both take courage today is an indication of how delicate and complicated the Islamist problem has become.

In daring to do both, Benedict succeeded in clarifying what the problem is, and where solutions might be found. It has been an important year in Christian-Muslim relations, and has established that relationship as a central element of Benedict’s pontificate. Call it Benedict’s “year of the Muslims” as it were; its consequences will be long-lasting.

Father Raymond J. De Souza served as the Register’s Rome correspondent from 1999-2003.