'Why there?" asks an ad on New York City's buses about the mosque to be built near Ground Zero. "Why so high?" the Swiss, who banned minarets this year, wanted to know. "Why so big?" complained the citizens of Munichin 2008, nixing a giant mosque in their midst. And "Why here?" asked German police this week, as they closed down the Taiba Mosque in downtown Hamburg.

Mosques are riling the soul of the West. In Hamburg, the story is not about turf but terror. The Taiba Mosque was previously known as the Al-Quds Mosque. This is where Mohamed Atta, the mastermind of 9/11, hung out with other co-conspirators. This is where Imam Muhammad al-Fazazi used to preach venom and murder throughout the 1990s, opining that "Christians and Jews should have their throats cut." In 2003, a Spanish court gave this pious cleric 30 years for planning attacks on Jewish institutions in Morocco.

So the mosque wasn't just a center of prayer. But the Hamburg police only kept tabs on the place, not touching it—not even after 9/11. Why not? Given the country's Nazi past, a government spokesman this week invoked the special protection that religious institutions enjoy in Germany. You can't just close them down. You need "intelligence work, and that can take time." Nine years, it turns out.

Meanwhile, a naturalized German from Syria, Mamoun Darkanzanli, had taken the pulpit. Investigators call Darkanzanli the "elder statesman of jihad" and have a fat file on him. They think that he is bin Laden's man in Germany, and that he also helped the Madrid train bombers of 2004. When Spain asked for his extradition, the German Constitutional Court said "nein." That would violate his rights as a German citizen.

Darkanzanli continues to live in Hamburg—unmolested and on welfare. And he knows his rights, wrapping himself in the constitution while preaching that Allah will kill the infidels. He isn't inciting violence, just spreading God's word. This is a problem that stumps counterterrorism officials around the Western world.

The local paper, the Abendblatt, calls the mosque a "Place of Pilgrimage for Jihadis." Why so? Manfred Murck, the deputy chief of the domestic security agency, explains: "Because it has the aura of the ƒË9/11ƒÍ assassins." Devotees of the 9/11 killers have come from all over on a tour of jihadism that starts in Hamburg, then proceeds to Madrid, then to London, where dozens were murdered in the tube in 2005. "Hey, I prayed where Mohamed Atta did . . ."

Others, according to the sleuths, used the mosque as a staging ground for "persons from the Former Yugoslavia, from Chechnya and from the Middle East." They would gather in the mosque and then depart on a mission from God.

But for authorities, it was still watch-and-compile. Why the raid now? This is where the Hamburg hub fits into the larger picture that now stretches across the Atlantic. Call it "home-grown terrorism," fed not only by immigrants, but also by converts. They speak and look like the locals. This is the new generation of jihadis—in the U.S. as well as Europe.

Suddenly, the bad guys were our own, a startling twist in the story. According to intelligence reports, 11 young men, most with German passports, left for a terror training camp in March of last year. The alleged leader was arrested this June along the Afghan-Pakistan border. The others are at large, perhaps going after German troops in Afghanistan.

So the preaching was hitting a raw nerve, and this summer the law changed. It is now a crime to hone terrorist skills in a foreign boot camp. The mosque was closed down because "young men were turned into religious fanatics there," according to Hamburg's interior minister, Christoph Ahlhaus. Do authorities have the evidence? We'll see.

Fanaticism itself is no crime, nor is discoursing on Allah's will. As in the U.S., a hateful ideology is no ticket to prison. Authoritarians have no qualms about equating ideology and intention. But Western liberal democracy obeys due process and the concept of "innocent until proven guilty." Words, as Oliver Wendell Holmes famously wrote for the Supreme Court in 1919, have to "create a clear and present danger" to be criminal. In that respect, the Germans may have become more American than the Americans.

So watch for the next installment of this drama, when the mosque's board might take the city to court. The bet is that we'll hear a dialogue like this. Judge: "Show me the evidence." Government witness: "Sorry, sir, we can't compromise our sources." Shades of Guantanamo. Case dismissed.

It would have been smarter to keep the mosque open precisely because it has been such a convenient source of information, with those terror tourists coming, talking and going. As the spokesman said: "Intelligence work takes time." Actually, it never stops, and good intelligence has proven the West's best weapon in the war against terror.

To boot, these folks know their rights. When the police demanded entry, the caretaker literally showed them the finger. Instead of breaking down the door and cuffing the brute, the police called a locksmith. Hamburg's police nabbed the computers. It would have been more efficient to hack them.

Mr. Joffe, the editor of Die Zeit, is a senior fellow at the Institute for International Studies and a fellow at the Hoover Institution at Stanford