When our flight landed in Tel Aviv, all the passengers were to deplane onto a waiting bus to be ferried across the tarmac to the terminal. All the passengers but four, that is. Three Palestinians and myself, an honorary Palestinian, were taken for further questioning. In the time we had together, we shared names and traded bios. Like me, they were students—studying in Egypt. Unlike me, they called this place home. Unlike me, they had a harder time getting in. For I was Muslim but also—and this confounded one Israeli soldier after another—American.

Before even reaching passport control, I was interrogated by two women who were very interested in determining if I was callous or dangerous. These were the facts they had to play with: I’d turned 21 a month before. I was single. I’d arrived via Cairo, where I’d already been studying for a month, and after this trip I’d go back for another month. I was studying Arabic. I was of Pakistani descent and roomed, in Cairo, with Haris, an Indian Muslim raised in Saudi Arabia, who was at NYU on a student visa. This most interested them, not just in Tel Aviv, but back in Egypt where the flight originated. Before I had even made it to the ticket counter, two men and a woman pulled me aside for questioning, which began and ended with my naming my friends. Sorry, Bradley, Jeremy, Jacob, and James. I needed white names.

Several hours later I was judged nonthreatening enough to enter. The Lonely Planet guide to Israel hadn’t bothered to include a section for traveling while indigenous or sharing the religion of the indigenous.

A shared taxi drove several of us 45 minutes across a gorgeous landscape to Jerusalem. I had never been to a place that made me feel more preternaturally uncomfortable. Many inhabitants were refugees who’d found a safe haven at the cost of expelling or suppressing that haven’s native population, a desperate conflict that any reasonable person would have seen coming from a century ago. Security delays had almost cost me my goal: a visit to the Old City, where I’d join Friday prayer services at the Noble Sanctuary—you might know it as the Temple Mount—which includes the Farthest Mosque, al-Aqsa, and the Dome of the Rock. When I finally arrived at the sanctuary, there must have been several hundred thousand people there.

In 619, at the lowest point in his mission, Muhammad was carried overnight from Mecca to Jerusalem. At the far edge of the Noble Sanctuary, Muhammad led every one of the prophets in prayer—one of the most powerful images of Muslim universalism, because prophets were sent to all peoples. Muhammad also came to the large rock, now covered over by one of the most beautiful buildings in the world, and from there he ascended into heaven.

Muhammad approached God’s throne, and in the intimacy of the Divine audience, he was informed that Muslims should perform salat (ritual prayer) 50 times a day. On his return, Muhammad shared word of the assignment with Moses, who urged Muhammad to talk God down to a more reasonable number. Moses and God went back and forth until five prayers were agreed on. Moses insisted that even this was overly much, but Muhammad couldn’t bring himself to return for another reduction. (I’m with Moses on this one.)

Every time Muslims pray, something of Jerusalem stirs within our hearts. It was from Jerusalem that Muhammad went up to God, after all, not Mecca or Medina. And each prostration—when the Muslim touches her forehead to the floor—is deemed a reproduction of Muhammad’s ascent, the closest she can get to God. The favored way of beseeching him, it represents the humbling of the self, but also Islam’s refusal to sunder external form from internal condition. You can understand the deep desire to be there.

I had made it in time to join Friday prayers. Mind you, most young men—my age, for example—weren’t permitted in, and almost every time I returned there during that trip, I had to argue my way in. But what I found behind checkpoints and past interrogations made it nearly impossible to leave.

Many places matter. Rarer is that place that feels deeply, truly holy. In the face of immense limitations on their freedoms, Palestinians had created here a religiosity that breathed through ancient stones. It felt like God was here, in a way I’ve rarely felt God. Was it in spite of the tragedy of Palestine, or because of it? It was a summer of intifada. And yet no Palestinian store owner or restaurateur or taxi driver ever took my money. “You are a guest in our home.” Their home. Where they were prisoners or refugees or second-class citizens.

There are many places where Muslims oppress other Muslims. Consider the history of the Kurds, as one example. Some governments do not allow their citizens to freely assemble, speak their minds, or even move about the country. Saudi Arabia, astonishingly, will not let women drive. Muhammad’s first wife, Khadija, was his employer. A later wife commanded an army in battle, and yet a restriction on women motoring is declared Islamic.

There are also many places where Muslims oppress people of other faiths. But these are harder for many Muslims to confront, because they involve a kind of self-critique that no people find easy to pursue. It’s the same reason many Americans might get whipped up into outrage over something occurring in Saudi Arabia, neglecting the fact that we have funded and armed and defended no other Muslim regime so strongly. Complicity has a funny effect on morality. But that doesn’t mean the Palestinians haven’t been wronged. The difference is how it’s played out.

Uighurs are persecuted by China, Chechens brutalized by Russia, and Kashmiris occupied by India, though none of these registers in quite the same way. Partly it’s religious—Srinagar is not in the Qur’an, nor is Ür¯umqi a sacred city. Partly it has to do with the outsized attention Israel receives in American media, and the country’s claims to sharing our values—if, of course, by “our values” you mean values we’ve tried very hard to abandon. It is also the lopsidedness of the conflict, which is frequently reported entirely backward in much of American media. However, it’s not only that. Who, really, is surprised by the crushing underfoot of small minorities by vastly larger states? What chance did Crimea’s Tatars have against Stalin, or the Rohingya on the fringes of Myanmar?

What boggles the Muslim mind—what represents to it, again and again, how far Muslim civilization has fallen—is the fact that a tiny state can occupy some of its holiest places and no productive action can be taken. That tempts some Muslims to ugly anti-Semitism—Israel must have far more power than we can see!—and others to impotent fury and rage. If Palestine is occupied, what does that say about those who seem to be able to summon nothing but indignation? What is it about modern Muslims that made us so unable to live up to our ancestors’ achievements, or our contemporaries of other backgrounds? To be Muslim is to be the stunted descendant of giants, to live in the ruin of your own civilization.

Seeing young men slammed to the ground for not answering a question quickly enough, a family uprooted from its home to make room for someone from somewhere else entirely, prompts a young man to ask why even if there may be tens of millions more like him, collectively they could do nothing. It is a question many Muslims feel, though they may be afraid to voice it, for fear of blasphemy: If Islam is so great, why are Muslims doing so badly? Maybe that’s why so many Islamic extremists find it so easy to kill fellow Muslims.

Yet to feel more keenly my own impotence was not among my reasons for going to Jerusalem. In fact, Jerusalem just amplified what I’d been feeling in Egypt ever since arriving there. In Cairo, I could construct no consistent spiritual practice, not even when surrounded by mosques and muezzins. But why? I wasn’t lazy. I was an active writer, a good student; I took part in student life, maybe more than I should’ve, and otherwise kept myself busy. When my anxiety ebbed, I’d work out; I read books religiously and watched movies superstitiously. Religion was the one part of my life where all discipline disappeared.

Egypt was a deep disappointment: a country with so much potential, not just stuck, but sliding backward. But who was I to have thought I could fix Muslims, or repair Islam, when I could not even overhaul myself? I wasn’t going to save the Muslim world through my pathetic efforts at NYU. I was the Muslim world. Afraid. Frozen. I could not move forward. I was not even inside of me. So many Muslims, it hit me, and yet so little changed. Whoever said there is strength in numbers hadn’t met modern Islam. We were an inversely proportional civilization. When we were few, we were bold. Now that we were many, we were all but moribund.

The only way I could think of making sense of this was by writing. I would write a novel. And I did. One of my characters, an adherent of a suspicious Sufi order that espoused outrageous beliefs about the end times, lit himself on fire before a McDonald’s on the Avenue of the League of Arab States, launching a popular revolution across the Near East, democracy, Islamist power, then disaster. The point was to tell a story about a time after people have had too much. The status quo was unsustainable. But what would follow? All that frustration had to go somewhere; it’d be directed out as much as in.

Suicide as regicide, down with the dictator and down with the people who let themselves be dictated to. Implosion and explosion, an energy radiating outward in devastating human waves, smashing apart what was outside while it broke apart what was inside. And yet I did not think these suicides were faithless. They were acts of devotion to God, sins that produced saints. If there is any consolation, my novel foreshadowed the Arab Spring, including the arrival of political Islam into power and the violence thereafter.

But writing about suicide? I conceived of these self-immolations as nakedly Abrahamic. In the Muslim tradition, the young Abraham, not yet a prophet, smashes his people’s idols to reveal their inconsequence and harmlessness. Unimpressed by this argument for radical monotheism, his people cast him into a bonfire, but God intervenes to seal Abraham off from the heat. He was in the fire, but not on fire.

I wanted to bring this tradition to my time What would it mean to cut the idol down, when the idol is now the self, man who has deified himself into the measure of all things? Would there be a self after, or would nothing remain because there was nothing there all along? But to kill oneself thusly, no matter how reverently, would still be sinful—it would demand the same bonfire Abraham landed in. There comes a point when sin can only lead to sin, and faith as well to sin. Was the course of the modern world simply incompatible with Islam, whose time had passed? Such a time would have to come to pass. Every great idea fades.

I could not otherwise explain why the Muslim world performed so poorly, or Islam affected me so unevenly. The two were one in my mind. I should have been able to force myself to wake up to pray the fajr. I did not know why I could not compel myself to pray five times a day when I was in a place overflowing with mosques, with minaret alarm clocks ready to remind me in case I had forgotten. I didn’t know why I would rather be flirting with a restaurant waitress than in the mosque studying the life of the Prophet. I should have simply been able to become Muslim. I should have pushed myself into obedience and, once there, settled down. And if I could not so reinvent myself, then what did that suggest about me? Light a fire and throw myself in. Die before dying, as the Sufi poets would say. If God willed, you’d live.

Haris and I reconnected as soon as we had set ourselves up back in Manhattan. He was downtown, but I was on the Upper East Side, in my first private apartment, shared with two friends.

When I got out of the subway one Tuesday, folks were congregating in the street, right off the curb, looking against traffic, their necks tilted at 45-degree angles. No one spoke. Until spoken to. A plane, someone told me, had flown into a World Trade tower. I assumed he meant a private plane. A terrible, horrible, but fully accidental accident. Thinking no more of it, I went to class—and found out, minutes later, just what had happened. Our professor, who’d suffered the shah’s authoritarianism and then Khomeini’s, let everyone except the Muslims and Middle Easterners leave. He shook his head. He was afraid. Not just because our nation had been attacked. But by whom. Be careful as you make plans to find your way home, travel in groups, accept that it would never be September 10 again.

On the way up the stairs and out of the building, I asked a friend if she needed help getting home. She hesitated, then looked me up and down and said, “Nobody knows I’m Muslim.” I was brown, bearded, and president of the Islamic Center at NYU, whose community was one of the biggest in proximity to a mass murder that’d be claimed in our name. She left, the professor began smoking on the sidewalk, and we all trembled as we stared up at the smoke that had devoured that perfect blue sky.

Where there were once two towers, now there were none. Then there were police cars—endless sirens. The city was on lockdown. Frightened and confused students filled Washington Square Park, classes ended, but the trains stopped, cell phone service was down, every television endlessly replaying a moment of catastrophe. We heard that Cleveland, Pittsburgh, Denver, and Seattle had also been attacked by jetliners. Car bombs had gone off in the nation’s capital. I knew, instantly, that this could only be al-Qaeda’s doing.

I rushed to our temporary prayer space, inside NYU’s Catholic Center, expecting to find Muslims, but instead we found an orthodox Jew. “What are you doing here?” I asked. We knew each other, but, as I wanted to subtly communicate, on this day he would probably not want to be found in a mosque.

“I figured if someone needed to get home, and wanted someone to walk her, I could come along. A hijab might provoke rage right now. Alongside a Jewish man, perhaps less so.” On that day of all days, he thought of us.

Before, the gaze of an omniscient God compelled me. There­after, the omnipresent eyes of a surveillance state would not leave me be. There would be nowhere we could go where we would not be asked to apologize. Many like me would come to regret wasting the time when we could have chosen to be different people. But those days were gone, never to come back.

This article is adapted from Haroon Moghul's forthcoming book How to Be a Muslim: An American Story (Beacon Press). Reprinted with permission from Beacon Press. A version of this article appears in the May 24 print edition under the title “How to be an American Muslim.”