If you followed the recently concluded Synod of Bishops at the Vatican, a meeting that brought together nearly 200 members of the hierarchy for discussion focused on the theme of family, you’re justified in having a case of whiplash after two weeks of high drama.

A preliminary report suggested a stunning shift in the Church’s tone on homosexuality, co-habitation, and other contentious issues. Just days later, a final report toned down much of the bold language that drew headlines as American Cardinal Raymond Burke and other conservative hardliners rejected the language as a “betrayal” of Church doctrine.

“We’re not giving in to the secular agenda,” Cardinal George Pell, an Australian archbishop now in charge of finances for the Vatican, insisted.

The reaction was fast and furious. “Catholic Bishops Scrap Welcome to Gays,” the Huffington Post harrumphed in a headline. “For Francis, a resounding defeat,” crowed Rorate Caeli, a traditionalist Catholic blog.

But conservatives who are doing a victory lap and progressives who are licking their wounds are missing the big picture about this meeting, and still fail to grasp the deeper meaning of the Francis papacy.

As seasoned Church observers have noted, the synod process itself was a major breakthrough for a Church that has often stifled debate or rubber-stamped a top-down message. Previous synods have been little more than staged events with the conclusion already written before anyone opened their mouth.

“Speak clearly,” Francis told the nearly 200 bishops at the start of this meeting. “No one must say, ‘this can’t be said.’ ”

The pope got what he asked for; afterwards, he said he would have been worried if there hadn’t been an animated debate. In a telling move, Francis ordered that even the edited language that failed to make the final cut be included in the concluding report along with vote tallies. (The section with more welcoming language toward gays and lesbians, for example, failed by only a few votes; language making it easier for divorced and remarried Catholics to receive Communion has a tougher road.)

And the drama is not over. When bishops meet in Rome next fall for the second and final act of this synod, you can bet there will be another robust conversation about how the Church can do a better job applying doctrine in a way that does not ignore the messy reality of human experience.

To really understand why this papacy is so revolutionary, you have to recognize that Francis is playing the long game. He is setting his vision on a different horizon than those who are stuck fighting trench warfare over a narrow set of hot-button issues.

While Catholics check off boxes on our ideological scorecards, Pope Francis is calling the Church to a profound spiritual conversion. His foes are clericalism, legalism, and anything that gets in the way of the joy of the Gospel. This is not a flashy corporate re-branding or a mere tinkering with tone. It’s a return to the radical values at the root of Christian faith.

When Francis of Assisi came along in the 12th century, his embrace of poverty, personal holiness, and peacemaking were a walking rebuke to an institutional Church mired in worldly corruption. The Franciscans, and later religious orders like Pope Francis’ own Jesuit order, inspired spiritual movements that still inspire people in ways that the fine print of the Church’s Catechism never will.

The pope’s closing address at the synod offered sober words that should caution against triumphalism on the left or right. Speaking to those he called “traditionalists,” Francis warned of a tendency toward “hostile inflexibility,” and of being “closed” in the letter of the law. Turning his attention to “so-called progressives and liberals,” the pope warned of a “deceptive mercy” that “binds wounds without first curing them and treating them.”

This is not the first time the pope has offered a challenge that cuts across ideologies. When he warns about an “economy of exclusion and inequality,” or questions the “crude and naive” trust some leaders place in “trickle-down” economics, surely Republicans who genuflect at the altar of Ronald Reagan are not getting a free pass. Democrats who cheer the pope for his progressive views on labor and the economy can’t ignore his description of abortion as part of a “throw-away culture.”

For Catholics, our Church should make us all a little uncomfortable. Otherwise, we simply use faith to baptize our own political agendas.

Reform is in the eye of the beholder. For rigid guardians of orthodoxy on the right, Pope Francis is playing with fire that threatens to burn down the house. Some liberals will never be happy until the Church ordains women, marries gays and lesbians, and endorses birth control. These are all legitimate debates to have, and Francis is clearly not afraid of discussion.

But this pope has his eye on a bigger prize. “We always need time to lay the foundations for real, effective change,” he told the Jesuit Antonio Spadaro. “The structural and organizational reforms are secondary …. The first reform must be the attitude.”

This slow, uneven journey will challenge our patience, defy easy labels, and make us all think a little harder. In the end, that might be just what the Church needs the most as a quiet revolution unfolds.

John Gehring is Catholic program director at Faith in Public Life, an advocacy group in Washington, and a former associate director for media relations at the US Conference of Catholic Bishops. He is writing a book about how the Francis papacy will affect the Church in the United States that will be published by Rowman & Littlefield next year.