Not long ago, after my 7-year-old son had battled the fierce dragon Latias at a Pokémon tournament in New Jersey, I took him to the hallowed site of another epic battle—Ground Zero—for a pilgrimage of sorts.

American flags flapped in the wind where the World Trade Center had once stood, the space now eerily empty, except for the construction beams traversing the sky. The bridge I had crossed every morning as a reporter at The Wall Street Journal hung in mid-air, going nowhere. The Greek church, in which I had found moments of quiet solitude during earlier times, was gone.

Born in 2002, my son is part of our world’s first post-9/11 generation, and this is the world he will inherit. My son Shibli has one word for the hijackers: “Nimwits.”

The Tea Party activists actually express the sentiments of Muslims such as myself who believe we have a serious problem inside our Muslim communities.

Our pilgrimage didn’t end there. I nosed our car three blocks north, and parked in front of an abandoned building at 51 Park Place, the faded letters of Burlington Coat Factory above the steel doors still advertising “Coats and more … for less!” This, I explained to my son, was where the couple we had just met at their modest Jersey City home wanted to build an Islamic center that some folks were now calling the “ Ground Zero mosque.”

Years earlier, I had for the first time prayed in the front row during congregational prayer at a retreat on the bucolic banks of the Hudson River. The prayer had taken place at a conference, organized by the couple, Imam Faisal Abdul Rauf and Daisy Khan, and, unlike typical prayer arrangements, the imam had accepted parallel prayer sections for women and men.

We then drove two blocks north to 20 Warren Street. There, our pilgrimage ended across the street from a wine store, New York Vintners, below the gay bar, the 2020 Club, where an open door with “MASJID” in red stick-on lettering stood propped open, beckoning the way to the another mosque, missed in the hoopla over the “Ground Zero mosque.” The MASJID Manhattan, known in the Muslim community as “the Salafi mosque,” I explained to my son, embracing the rigid interpretation of Islam that is known as Wahabism.

Sitting in our car, a member of “the Salafi mosque” eyeing us, I told my son about the hurt feelings of the victims of 9/11 families for the other mosque going up near Ground Zero; the fears of activists who belonged to something called the Tea Party; and the rivalries and potential for a “good mosque” and a “bad mosque.”

For weeks since our pilgrimage, the furious debate over the Ground Zero mosque has vexed me.

There is a war raging in the world today, not just between America and radical Muslims in Afghanistan and Iraq, but within Islam itself. The two mosques—one a dream, the other a reality—belong, on paper at least, in the same neighborhood—blocks apart, and just blocks from where the World Trade Center once stood. Yet, the worlds represented by these two mosques could not be further apart.

• America’s 30 Muslim Capitals• Sam Harris: Obama Is Wrong in Supporting the Mosque• M.J. Akbar: Why the Mosque Hurts the RightWe’re not being honest in our Muslim community about the violent ideology inside of our Muslim world that needs to be defeated, and so the war has spread beyond our community to include the Tea Party activists. In the name of political correctness, too many inside our Muslim community have been apologists for Islam, feeling defensive, but not being as brutally honest as the world needs us to be about this problem.

The Tea Party activists actually express the sentiments of Muslims such as myself who believe we have a serious problem inside our Muslim communities.

I may not share their political language but I believe their fears are legitimate. And for those who disagree, I have just two words: Faisal Shahzad, the alleged would-be Times Square bomber.

Liberal and progressive Americans and their organizations have dropped the ball in having a nuanced, intelligent critique of extremist Islamic ideology, currying pluralism points instead in the name of interfaith relations.

In their PR campaign to defend the name of Islam, mainstream American Muslim organizations such as the Council on American-Islamic Relations have failed to acknowledge there is an interpretation of Islam that preaches violent jihad against the West. Their mantra has become this: “Islam is a religion of peace,” and they try to explain away men such as the alleged Fort Hood gunman, Major Nidal Hassan, by saying, “He isn’t Muslim.” Now they are jumping onto the Ground Zero bandwagon in the name of religious freedom.

I was born into a conservative Muslim family from India, where my mother grew up wearing the full-on black shroud and face veil, called the niqab, and emigrated to the U.S. with my family when I was 4. I remain a Muslim, and I wish I had had a mosque that welcomed people like me, without the prohibitions and edicts of the “the Salafi mosque,” which declares on its website that celebrating “non-Muslim festivities” such as Christmas is “forbidden,” and that among the “seven conditions for a women’s dress” the fourth item is: “The female clothing must not resemble the man’s clothing.” “The Salafi mosque” relegates women to the shadows and preaches isolation rather than assimilation.

We need an expression of institutional Islam that is moderate, progressive and liberal. We don’t have it yet. There is only one mosque in America where women can pray in the front row. It’s in Toledo, Ohio.

And the organizers of the mosque on Park Place are folks I recognize. One of the owners of the property for the planned mosque is a businessman, Sharif El-Gamal, who is married to Rebekah, an American woman from East Hampton, who converted to Islam, but who still wears shorts and tank tops in the photos posted on her Facebook page. She reads Goodnight Moon to her baby Jennah, her daughter Sarah, a toddler with locks of curly blond hair, and Peanut, the family cat. The couple and other organizers, such as my friend Ameena Meer, an advertising executive who once dated Salman Rushdie, want a moderate imam at the mosque, and have found one in Imam Faisal Abdul Rauf.

The right inside the Muslim community and outside has defined and controlled the debate. It’s time that all of us find the spiritual courage to ditch the demonizing, on the one side, and the apologizing, on the other side.

After our pilgrimage, I asked my son, Shibli, how he thought this conflict inside and outside our community should be resolved. His civilized solution? “Rock, paper, scissor—best of three wins.”

Asra Q. Nomani is the author of Standing Alone: An American Woman's Struggle for the Soul of Islam. She is co-director of the Pearl Project, an investigation into the murder of Wall Street Journal reporter Daniel Pearl. Her activism for women's rights at her mosque in W.V. is the subject of a PBS documentary, The Mosque in Morgantown. She recently published a monograph, Milestones for a Spiritual Jihad: Toward an Islam of Grace. asra@asranomani.com