Ian Johnson abhors pack journalism. Instead, he prefers to investigate the margins of major news stories. In A Mosque in Munich, this predilection serves him well. Based in Berlin and Beijing, he speaks fluent German and Mandarin, and holds an advanced degree in Chinese Studies. With equal tenacity and lack of bluster, however, he also pursues the development of radical Islam in Europe. Mostly by accident, the veteran journalist stumbled upon one of the largest untold stories of the last fifty years: how, with help from Nazis and the CIA, radical Islam first established its foothold in the West, and planted its roots firmly in Germany.

Johnson begins decades before the now-familiar Cold War narrative of the 1980s. In that decade the United States began to back the Muslim holy warriors, mujahideen, in their fight against the Soviets in Afghanistan. But as Johnson’s investigative work definitively shows, America’s efforts to use the religious and political fervor of Islam to its own ends followed a Nazi program intended to do much the same thing during World War II. This was a program, Johnson writes, which Hitler “explicitly blessed,” saying, “I consider only the Mohammedans to be safe. All the others, I consider unsafe.”

In the eastern regions of the Soviet empire, where the Nazis were more interested in oil than ethnic cleansing, the Third Reich mobilized Muslims and other ethnic minorities to fight for the liberation of their homelands. The Nazis plucked Muslims from German prisoner-of-war camps: some Muslims became German soldiers; some, members of the SS; some, professional propagandists. Although rumors and half-truths about this historic collusion have long existed, Johnson does the painstaking archival work of retracing the lives of these largely unknown Muslim Nazis, and pieces together their lives compellingly.

Once World War II ended, many of these men, stuck in Germany and having lost their homelands, found a new employer: the United States. Radio Liberty, the lesser-known stepsister to Radio Free Europe, was the CIA’s effort to broadcast anti-Soviet propaganda into Eastern Europe. In order to reach the thirty million Muslims living within the Soviet Union, the Americans turned to many of these former Nazi sympathizers. The idea, from the 1940s onwards, was to use Islam to undermine the Soviet system. Islam, American officials mistakenly believed, was the ideal antidote to godless communism. Although many of Johnson’s readers will know this story in broad strokes, no book before this one so deftly traces the history of this ideological misstep. And no one, until Johnson, has traced how far back this error in judgment went.

It is not just Johnson’s investigative reporting that makes this book important. He also has a gift for historical narrative. He structures his cloak-and-dagger tale around a series of absurdly colorful characters, from the famous Said Ramadan to the little-known figure of Ahmad Kamal, whom Johnson calls an “one of the most charismatic figures in America’s effort to harness Islam.” Between writing thrillers and working as a spy, Kamal moved from California to Indonesia organizing disaffected Muslims. His eyebrow-raising antics make more familiar Cold War cowboys, such as Charlie Wilson, look like all hat and no cattle. (To give these antics away here would be unfair to Johnson’s meticulous biographical research; read the book.)

A vein of dark humor runs throughout the book, as Johnson points out America’s early and later missteps vis-à-vis Islam with a kind of fatalistic legerdemain. Since this story unfolds so much at the margins of American foreign policy, it might seem rather mundane. (My biggest criticism of the book is its rather flat-footed title.) But just when this reader’s eyes would start to glaze over at all the exotica, Johnson usefully steps back to locate his particular story within the context of today’s unavoidable confrontation between the West and certain strains of Islamic thinking.

Unlike many of his contemporaries, Johnson takes the time to define the terms that he uses. Most notable is his discussion of Islamism, a word we often encounter but rarely hear properly explained. Who are all these “Islamists,” really? This is one of the helpful moments at which Johnson breaks his narrative to tell us clearly: “Islamists differ from traditional Muslims because they use their religion in pursuit of a political agenda, via either democracy, or violence.” In his strong but unassuming way, Johnson tells us something that is true and significant: “Implicit in Islamism is a rejection of Western society and its values.” This is one of the most essential—and uncomfortable—truths in the book. Yes, the West has unwittingly fed the rise of political Islam. And still worse, America continues to misunderstand something even more fundamental about the politics of Islamism: much of its ideology is born out of opposing the West.

The question follows, Can the West coexist with Islamists? Johnson reveals that the current ideological fault lines are more insurmountable than we know. Appeasing Islamists is ill-advised policy. But America continues to support groups such as the Muslim Brotherhood anyway. There are two Muslim Brotherhoods, he argues, one in the West and another in the rest of the world. The former is much more perilous to American interests. Still, out of ignorance and laziness in part, many American bureaucrats and foreign policy-makers turn to the best-looking business-suited Islamist leaders as allies. Many are tied to the Muslim Brotherhood, which, in the West, is a deliberate proponent of radical Islam. The United States does this, in part, because it’s easier to turn to self-appointed spokesmen for the world’s Muslims than to reach out to far less media-savvy members of civil society—Muslim groups that aren’t so slick and organized by ordinary people. “Ordinary people are messy,” Johnson puts it.

The book is funny and tragic and peaks toward the end when Johnson takes us along on his interviews with contemporary members of the European branch of the Muslim Brotherhood. One day in Cologne, Johnson rides along in the BMW’s passenger seat of Ibrahim El Zayat, a young Islamist who leads many of Germany’s Muslims. Zayat is hugely controversial, and it is hard to know whether or not he condones the use of violence based on some of his murky associations. When Johnson points this out, Zayat points right back at Johnson. “A lot of people say that Ian Johnson is a CIA agent because you write so little.” “My boss says that too,” I say. “You should write more. Sloth is a sin.”

At the end of the ride, Zayat answers one of the most important riddles as to why the West gets it wrong when choosing Islamic allies. We ask the wrong questions about who they are and where their ideas come from. It is really a matter of research: of taking the time to get our facts right, as Johnson clearly has. When he asks Zayat about his alphabet soup of radical affiliations, Zayat replies: “I don’t deny that I’m in these groups.… When I’m asked clearly, then I answer.” The challenge for us, then, is to get our questions right—and this Ian Johnson has done masterfully.

Eliza Griswold is the recipient of a 2010 Rome Prize. She is a fellow at the New America Foundation. Her forthcoming book The Tenth Parallel: Dispatches from the Fault Line Between Christianity and Islam will be published early this fall.