In March, the Supreme Court heard oral arguments in Sebelius v. Hobby Lobby, one of the most-followed cases of the year. The Oklahoma craft-store chain, alongside a much smaller Mennonite cabinetmaker, was fighting the provision in the Affordable Care Act that requires employers to provide no-cost birth control through their insurance plans. Hobby Lobby and its co-plaintiff argued that providing contraception-specifically, four hormonal contraceptives that some Christians insist cause abortion-is an unacceptable violation of their companies' religious standards.

It's an unprecedented complaint. A for-profit company has never been granted a religious exemption, much less a corporation like Hobby Lobby, which has 23,000 employees. If Hobby Lobby is successful, religious business owners will have much broader leeway over their employees' health-care plans. But the case also raises a basic constitutional question: How should we weigh religious conscience against laws that apply to everyone? A ruling in Hobby Lobby's favor would give believers wide latitude. Religious scruples could be invoked to duck all manner of laws-even anti-discrimination statutes.

At the heart of the Hobby Lobby case are the craft store's owners, the Greens, a multigenerational family of evangelical Christians. On the plaintiffs' website-a glossy scrolling page where supporters are encouraged to "donate a tweet" to the Greens' cause-their story unfolds in a video. "In 1970, with only $600 and unwavering faith, David and Barbara Green began a small business out of their garage," the voiceover begins. "What's at stake here," the video continues, "is whether you're able to keep your religion when you open a family business."

The Greens are the public face for the case, but a little-known nonprofit law firm called the Becket Fund for Religious Liberty is its driving force. Even Hobby Lobby's detractors agree that the Becket Fund's lawyers are among the country's most capable defenders of religious rights.

If the Supreme Court grants the company its exemption, it will be in large part because of the Becket Fund's masterful telling of the Greens' story.

The fight over the Obama administration's alleged infringement on religious freedom is Becket's first extended turn in the national spotlight since it was founded in 1994. For more than two years, the fund-with a budget of less than $4 million and 11 lawyers on staff-has constructed the legal argument against requiring religious organizations to comply with the contraception mandate. Forcing any organization to subsidize health-care plans that defy its faith is, the fund claims, a breach of the Religious Freedom Restoration Act, a statute passed in 1993 that allows believers to demand exemptions from laws that place a "substantial burden" on their religious rights. Late in 2011, Becket filed the first suit against the mandate on behalf of Belmont Abbey College, a school founded by Benedictine monks. Since then-perhaps encouraged by its success in lower courts-the fund has agreed to represent six more nonprofits.

The Hobby Lobby case is more ambitious than these challenges. It's one thing to argue that a Catholic college's daily operations are imbued with a religious ethos. It's another to contend that a corporation, competing in a secular marketplace, is so fundamentally guided by its owners' faith that it should enjoy religious-liberty rights.

Becket's attorneys are applying a similar logic in other cases. Among their clients are religious business owners, almost always Christian, who face discrimination charges for refusing to provide services associated with same-sex weddings. These lawsuits are the cousins of the so-called conscience cases, in which a religious pharmacist who declines to sell emergency contraception runs afoul of state law. Becket is litigating a couple of those, too.

The Becket Fund has always insisted that it is that rare type of religious-liberty advocate: an organization with no partisan allegiances, committed to defending faiths of all sizes with equal zeal. Kevin J. "Seamus" Hasson, the group's founder, liked to boast that Becket defended the "religious rights of people from 'A to Z,' from Anglicans to Zoroastrians." The phrase quickly became the group's motto. Lately, it's begun to serve as a kind of talisman to ward off the accusation that Becket is taking sides in the culture wars.

Charles Dharapak / AP Photo David Green, founder and chief executive officer of Hobby Lobby, second from left, walks with his wife Barbara, center, and members of their family as they acknowledge a cheer from demonstrators in the crowd as they descend the steps of the Supreme Court in Washington, Tuesday, March 25, 2014, after the court heard oral arguments in the challenges of President Barack Obama's health care law requirement that businesses provide their female employees with health insurance that includes access to contraceptives.

To some, the decision to sponsor politically charged lawsuits like Hobby Lobby's signals a shift in the fund's strategy. By choosing cases that will undermine the Affordable Care Act and slow the progression of same-sex marriage, critics contend, the fund has become ideological. The money seems to point in that direction. Although its supporters were always conservative, right-wing activists began to fill Becket's coffers just as the contraception-mandate litigation took off. The group's contributions and grants rose by more than 60 percent in the year after the Belmont Abbey suit was filed.

In 2012, the Becket Fund received almost a quarter of a million dollars from DonorsTrust, a shadowy middleman used to funnel money from benefactors like Charles and David Koch to conservative think tanks and advocacy groups.

(The Becket Fund declined repeated requests for comment about its work and funding.)

Not everyone agrees that the fund is tacking right. "It's myopic to characterize Becket through the lens of the controversies that happen to be going on right now," says Rick Garnett, a professor of law at the University of Notre Dame, who has co-written Supreme Court amicus briefs with Becket attorneys. "Their willingness to defend somebody's religious freedom has never depended on whether or not they agreed with that person's claim."

But Douglas Laycock, a professor of law at the University of Virginia who frequently partners with the fund, has noticed a troubling change. "They've bought into some of that culture-war, anti-Obama rhetoric from the right," he says. "The legal work is still very good. The political statements are much more heavy-handed."

The Becket Fund was established at the height of a bipartisan backlash to a Supreme Court decision written by, of all people, Antonin Scalia. In 1990, Scalia authored the majority opinion in Employment Division v. Smith. The case revolved around whether two drug counselors, who were fired from their jobs at a private rehabilitation clinic in Oregon for using peyote as a sacrament during a Native American religious ritual, could claim unemployment insurance. The state of Oregon argued that because peyote was illegal, they had been fired for cause. Unemployment benefits were out of the question.

Scalia agreed. Rejecting the drug counselors' claim that their peyote use was protected under the First Amendment, he explained that because the drug statute was "neutral," singling out no specific religious tradition or practice, the counselors couldn't claim an exemption. After all, the court had ruled in the past that the constitutional right to freely exercise religious beliefs did not permit citizens to violate laws against polygamy or child labor. Why should illegal drugs be different? A ruling in favor of the counselors, Scalia wrote, "would open the prospect of constitutionally required religious exemptions from civic obligations of almost every conceivable kind."

The decision was radical because it overturned the Supreme Court's old test for determining whether free-exercise claims held sway.

Before, the government had to establish that it had a good reason for burdening religious liberty. Now, politicians would only need to prove that they hadn't isolated one tradition for special treatment. "The identical principle will apply to a law that criminalizes killing an animal in any but a statutorily prescribed way, with no exception for the way prescribed by Jewish law," wrote Theodore Mann, a prominent lawyer, in a letter to the New York Times. "Roman Catholics, Protestants and Jews may feel that their respective organizations have sufficient power to protect themselves at every legislative level. But the worm turns."

Ron Edmonds/AP Photo

Months before Scalia handed down his decision in Smith, a Laotian Hmong couple was in the last stages of a religious-liberty lawsuit against the Rhode Island medical examiner, who had performed an autopsy on their son against their will. Hmong religious tradition forbids postmortem incisions; adherents believe that mutilation of the body keeps the soul from moving to the next world. Because there was no public-health reason for the autopsy-the young man had died unexpectedly of a seizure-the judge ruled that the medical examiner had erred. The burden on the family's religious beliefs outweighed the government's interest in determining why their son died. Before the judge could determine the damages, however, the Smith ruling was released. With great regret, the judge withdrew his verdict. Although the medical examiner had infringed on the Hmong family's religious freedom, he explained, the new standard imposed by Smith meant that the autopsy was no longer a violation of their constitutional rights.

Fearing similar outcomes in cases in which religious minorities would once have been protected, a coalition of religious and secular organizations banded together to restore the old standard. The bill that resulted-the provocatively named Religious Freedom Restoration Act-passed late in 1993. Only three senators voted against it. Acknowledging the abnormally bipartisan alliance at the signing ceremony, Bill Clinton joked, "I suppose the power of God is such that even in the legislative process, miracles can happen."

When the Becket Fund opened in 1994, it was entering a crowded field. Half a dozen law firms intent on preserving religion's place in the public square had been founded in the late 1980s and early 1990s, many with close ties to the Christian right. Pat Robertson launched the American Center for Law and Justice in 1990; almost immediately, its lawyers began to urge students to initiate prayer at public-school graduation ceremonies. James Dobson created the Alliance Defense Fund (now the Alliance Defending Freedom) in 1994 as a safeguard against liberal attempts to "crush religious expression."

These firms were bankrolled by conservative donors and shared the bipartisan religious liberty coalition's concerns only as they pertained to the freedom of Christian expression. Robertson and Dobson, disturbed by a series of lawsuits beginning in the 1960s that eroded the tradition of prayer in schools, were unabashedly ideological, promoting what Dobson's group called the "Body of Christ in America."

The Becket Fund's founder, Kevin Hasson, insisted that his firm would be different. Hasson himself stood out as an intellectual force, a lawyer in his thirties with a philosopher's heart. He had earned a master's degree in theology from Notre Dame, his undergraduate alma mater, and toyed with the idea of a doctorate before enrolling in law school. After a brief stint in the Reagan administration tending the Justice Department's religious-liberty portfolio under Samuel Alito, he went into private practice with a firm that represented the Catholic Church and its affiliates.

Hasson feared that the creeping wave of secularism could wash religious expression out of American life. But like many Catholics, he was also keenly aware of the cost of imposing a state religion. In the 19th century, when Catholic immigrants began to land in cities like Boston and New York, Protestant leaders insisted that Catholics, by pledging loyalty to the pope, threatened democracy. Riots broke out in Philadelphia in 1844, fueled by rumors that Catholic teachers were trying to keep the Bible from being read aloud in schools. The Ku Klux Klan included Catholics among its targets well into the 20th century. In 1949, American Freedom and Catholic Power, a polemic that pointed to the Church as a fundamental threat to American democracy, shot to the top of the best-seller lists.

From its inception, the Becket Fund was infused with a strong Catholic presence. Hasson named the organization after a saint: Thomas à Becket, a 12th-century English archbishop murdered by four of Henry II's knights after refusing to allow the king to dictate the affairs of the Church. Leading conservative Catholic intellectuals like Mary Ann Glendon and Robert P. George joined the Becket Fund's board.

Unlike Dobson's and Robertson's groups, which sought to restore a version of Christian hegemony, Hasson's view of religious liberty drew on a long tradition in Catholic thought, which positioned religious freedom as a natural right. Ordained by divine law, rather than human justice, it required special protection. It wasn't enough to say that because the United States was a Christian country, religion should be central to public life. Instead, a robust conception of religious liberty needed to stress that faith was a natural part of culture. Confining religion to private spaces would muzzle a defining element of existence.

If the Becket Fund initially had a bias, it was more legal than ideological.

Hasson chose cases that he felt were infringements on the clause of the First Amendment that protects citizens' rights to practice religion freely; he was less interested in its other provision, which forbids the establishment of a state religion.

Association with one clause or the other tends to indicate a partisan divide-liberals want religion out of government and conservatives want government out of religion-but Becket's ecumenical commitments set it apart. Dobson's and Robertson's law firms had little interest in defending anyone but Christians. The Becket Fund, by contrast, offered its services to aggrieved believers of all stripes.

Hasson maintained from the beginning that his firm would be beholden to neither party. Rick Garnett was a young lawyer living in Washington, D.C., when he met Hasson in the mid-1990s. "I was impressed by his commitment to religious liberty as a human right," Garnett says. "It couldn't be reflected through a culture-wars lens if it was going to survive. It had to have universal and bipartisan appeal." Without access to Christian-right donors, the Becket Fund operated on the force of Hasson's personality. Witty and genial, Hasson sprinkled his briefs and press releases with jokes and asides. Much of its early funding, which allowed Hasson to rent a one-room office in Washington, D.C., and hire two lawyers, came from the Knights of Columbus, the right-leaning Catholic lay organization.

Early on, Hasson took cases that gratified and vexed advocates on both sides of the political aisle.

Becket defended a Knights of Columbus chapter in Trumbull, Connecticut, whose attempts to put a creche in the center of town were being stymied by church-state separationists. In 1998, Hasson argued before the U.S. Third Circuit Court of Appeals alongside attorneys from the American Civil Liberties Union (ACLU), demanding that the Newark police department drop its prohibition on beards for the sake of its Muslim officers.

The Becket Fund seemed well positioned to use the newly passed Religious Freedom Restoration Act to protect believers' rights. But in 1997, the Supreme Court interrupted. In Boerne v. Flores, a Texas archbishop sued local zoning authorities who had denied his church a permit to expand, using the statute to challenge their decision. The court responded by striking down the act as it applied to the states, limiting its authority to the federal government. Now, only federal prisons had to allow Muslim inmates to fast during Ramadan; school districts were free to bar religious head coverings in the classroom.

Advocates responded with a two-pronged strategy: urging states to pass their own version of the original religious-freedom law and re-establishing a federal religious-freedom statute that explicitly covered states and localities. The landscape had changed in four years, though. In a handful of cases, landlords who refused to rent to unmarried couples had successfully obtained exemptions from housing-discrimination laws, using a religious-liberty defense. Civil-rights watchdogs voiced fears that seem prescient today: What if a landlord or employer, citing their religious principles, used the law to discriminate against gays?

The bipartisan coalition that had pushed for the original religious-freedom law began to crumble. In 1999, the House passed a bill that would prohibit state and local governments from burdening religious exercise without a compelling reason, but it never came up for a vote in the Senate. The coalition instead proposed a narrowly tailored bill called the Religious Land Use and Institutionalized Persons Act, which limited the "compelling interest" standard that Scalia had erased in Smith to zoning claims and complaints from state prisoners.

With the passage of the new law, the Becket Fund came into its own. In 2003, it won a zoning permit for a nondenominational megachurch in Orange County, California, which wanted to build a larger worship space. Church leaders had set their sights on a former racetrack where county officials-unwilling to turn over prime real estate to an institution that wouldn't pay property taxes-had hoped to attract Costco. In 2006, Becket's attorneys advocated on behalf of a prisoner who wanted to keep an Odinist crystal in his cell; in the same year, the fund defended a large evangelical prison ministry's right to receive money from the state.

The organization also took on cases that aided a quintessentially conservative cause: school vouchers. The Lynde and Harry Bradley Foundation-a right-wing foundation and one of the Becket Fund's most consistent donors-poured millions of dollars into pro-voucher initiatives beginning in the 1990s. In the litigation that followed this experimentation with taxpayer subsidies to private (often religious) schools, the Becket Fund helped develop a powerful legal argument in support of vouchers.

Dozens of states had dusty statutes called "Blaine amendments" attached to their constitutions, which forbade the use of public funding for sectarian schools and institutions. The amendments dated back to the 19th century, when Catholic families-angry about the prevailing norm in public schools that required children to read a Protestant version of the Bible and recite Protestant prayers-began to seek government funding for parochial schools. The Blaine amendments were an unapologetic attempt by Protestant politicians to prevent the "Catholicization" of American education. In several Supreme Court amicus briefs, the Becket Fund argued that the Blaine amendments, aberrant relics of a nativist past, could not be applied to contemporary schooling debates.

The voucher cases fit into the fund's larger narrative of protecting religious minorities from discrimination. To them, Catholics' persecution was still alive in the Blaine amendments. But the fund also defended conservative causes that had little to do with religious minorities' rights. In these cases, believers' traditional values were pitted against social change. In 1999, Becket lawyers mediated an employment dispute between the Air Force and Lieutenant Ryan Berry, a Catholic nuclear missileer who was reprimanded by his commanding officer because he refused to share an underground silo with a female colleague on the grounds that such close quarters would "occasion sin." The following year, Becket filed an amicus brief in Boy Scouts of America v. Dale, arguing that the New Jersey Supreme Court had overstepped when it ordered a local chapter to reinstate a scoutmaster who had been dismissed because he was gay.

At first, these cases were only a fraction of the Becket Fund's work, which was dominated by land-use struggles. But the balance was shifting. Three years after the first gay couples were married in Massachusetts in 2004, a Becket attorney argued in the Harvard Journal of Law & Public Policy that the new "legal reality" of same-sex marriage would "erode traditional deference to religious sensibilities." In other words, gay rights and religious liberty would become a zero-sum game. What gay couples gained in social acceptance, the faithful lost in freedom of conscience. By sanctioning nontraditional sexual relationships-epitomized by the legalization of gay marriage-the government was forcing believers to enable activities they viewed as immoral. If these changes were inevitable, politicians were duty-bound to carve out large exemptions for religious individuals and institutions.

In 2005, the Becket Fund convened a conference on same-sex marriage and religious liberty, assembling scholars to engage in a thought experiment. They were told to begin with the assumption that the legal definition of marriage had been expanded to include same-sex couples. What disputes would emerge, and how could they be resolved? Douglas Laycock, who attended the forum and later compiled essays from participants into a book, felt optimistic about the outcome. "I really hoped the issue could be resolved with some goodwill from both sides," he says. At the time, Anthony Picarello, a Becket attorney who went on to serve as general counsel for the United States Conference of Catholic Bishops, was less sanguine. "Legal redefinition of marriage," he said, "will be an engine of religious freedom litigation for years to come."

On the last day of 2013, just hours before the contraception mandate was scheduled to go into effect, the Supreme Court gave another one of the Becket Fund's clients, an order of nuns called the Little Sisters of the Poor, a temporary stay. The Obama administration had offered a compromise for religiously affiliated nonprofits like the Little Sisters, which operates nursing homes for impoverished seniors. They could opt out of the mandate by filling out a form that declared their objection to providing no-cost contraception, which they would send to their insurer. In response, the insurer would pick up the cost of the birth control. Mark Rienzi, the Becket Fund lawyer representing the Little Sisters, argued that this accommodation was unacceptable. Even if the Little Sisters were not directly subsidizing their employees' birth control, signing the form would trigger a process that would still result in no-cost contraception for their employees. The nuns could not sign the form in good conscience; it would make them complicit in the government's program to make employers foot the bill for their workers' birth control.

Michael Sean Winters, the influential left-leaning Catholic journalist, was disturbed by this logic. In a blog post for the National Catholic Reporter, he accused Rienzi of lying.

It was unlikely, to Winters's mind, that the Little Sisters had instinctively felt that signing the document would stain their conscience. "There are varieties of mendacity," Winters wrote.

"When I say the permission-slip language is a lie, it is a very specific type of lie. It is not like Bill Clinton saying, 'I did not have sex with that woman,' when, as we all subsequently learned, he did have sex with that woman. No, this lie is more like the lies of those who deny climate change. It is the lie of the zealous."

Others argue Becket's emphasis on the rights of the Little Sisters or the owners of Hobby Lobby has elided the necessary corollary: If they win their exemption, their female employees will be penalized. To Frederick Gedicks, a professor of law at Brigham Young University Law School, this lack of empathy betrays an "entitled" mentality, where religious institutions are considered to have consciences at the expense of individuals. "I think that if you care about liberty, you have to care about everybody's liberty and not just your own liberty regardless of the expense to others," he says. "It's a violation of those women and families' religious liberty to have to absorb the cost of the exemption."

Today's debates over religious liberty are, in many ways, a cipher for deeper anxieties about shifting sexual morality. In the conservative narrative of the conscience cases, the courts are asked to determine the extent to which religious people should be forced to bow to a secular liberal orthodoxy that sanctions immoral sexual behavior. In this story, Christians are an embattled minority, which helps explain why the Religious Freedom Restoration Act seems like a logical defense for people who believe that traditional sexual values are being crushed. It also helps explain why the Becket Fund-founded on the notion that "religious expression is natural to human culture"-is at the forefront of what has been cast as a last-ditch effort to preserve an elemental right.

In 2011, Hasson's advancing Parkinson's disease forced him to step down as president; he was succeeded by William Mumma, a former hedge-fund executive. Both see the fund as a bulwark against the tide of disaffiliation that has drawn nearly one in five Americans away from organized religion over the past two decades. In his book,The Right to Be Wrong: Ending the Culture War over Religion in America, first published in 2005 and released in a new edition in 2012, Hasson contends that religion is the wellspring of morality. His argument is pluralistic-it's your right to be wrong about the god you worship-but there's little room for nonbelief. The spread of secularism isn't just a demographic fact; the more people profess to have no religion, the further America drifts from its moral center.

"The way that religious fights have played out over the centuries has been in terms of Christians against Muslims, Muslims against Christians, Catholics against Orthodox," Hasson said in a speech to the Heritage Foundation in 2012. "But never before have we had a situation where the fight is not between principled people fighting over their principles. The fight is now between people who believe in something and people who believe in precisely nothing. They are nihilists, and this is a threat that is simply unprecedented."

If religious liberty has become the latest flash point in the culture wars, groups like the Becket Fund are not wholly to blame. Earlier this year, when legislators in a handful of Republican-controlled states, including Kansas and Arizona, introduced modifications to their versions of the Religious Freedom Restoration Act, LGBT-rights groups lambasted the changes as legal loopholes for discrimination against gay patrons. These bills ultimately failed, but Mississippi, which had no such law on the books, managed to pass its own version of the religious-freedom act. GLAAD, a gay-rights organization, condemned the law as a "thinly masked attempt to discriminate against LGBT people under the guise of 'religious freedom.'"

K. Hollyn Hollman, general counsel for the Baptist Joint Committee for Religious Liberty, a legal advocacy group that promotes both free exercise of religion and church-state separation, says that the highly publicized campaigns against these laws are feeding a wider perception that religious liberty and civil rights are diametrically opposed. "There is not a single case where this law has been used to deny someone services in a business environment," she says. "The law and religious liberty more generally are not the enemies here." But she believes that some of the Becket Fund's aggressive rhetoric is equally unwarranted.

"The government sometimes has interests that are going to conflict with someone's religious beliefs and practices, and that's not alarming."

Even in the midst of its contraception-mandate litigation, the Becket Fund has maintained its old commitments. It is currently collaborating with the ACLU on behalf of a Jewish prisoner in Florida who was denied kosher food. In 2012, the fund took on a high-profile land-use case involving a mosque and Islamic community center in Murfreesboro, Tennessee. "We didn't make conservatives very happy when we took on that case," says Robert P. George, a Princeton professor and longtime board member. "But we did it-even though we risked losing donors-because it aligned with our robust conception of religious liberty."

But Becket is also accepting edgier cases than it once did. Late last year, the fund announced that it would defend a Wisconsin priest who is endorsing candidates from the pulpit based on their stance on abortion. Churches, as nonprofit organizations, are forbidden from engaging in this kind of politicking, although the IRS's enforcement is lax. In 2008, the Alliance Defending Freedom organized an annual "Pulpit Freedom Sunday," during which dozens of preachers across the country defied the ban, hoping to prompt a court challenge that would vindicate their actions. By frequently announcing his support of candidates, the Wisconsin priest is engaging in a more extreme version of that protest. "A few years ago, I would have said Becket wouldn't go anywhere near that kind of case," says Barry Lynn, executive director of Americans United for Separation of Church and State. "It's too fringe-y. This is a pastor who's breaking the law to prove a point. I would have thought they'd leave that to the Alliance Defending Freedom."

Regardless of the outcome in the Hobby Lobby case, it's hard to imagine that Becket could return to its role as the quiet arbiter of free-exercise disputes-nor is it likely that it would want to. "Becket didn't use to be a place that was allergic to nuance," Winters says. "But now they're in an echo chamber, making arguments that diminish the issue rather than moving it forward. Nobody's looking for a real solution anymore."

This article is from the July/August issue of The American Prospect magazine.