From a father in Missouri who’s looking to keep his daughters from accessing birth control, to the refusal of key contraception mandate plaintiffs to accept the Obama administration’s latest “accommodation,” the Hobby Lobby decision continues to reverberate.

But while the Green family who filed the Hobby Lobby suit objecting to the mandate are evangelical Christians, the road to Hobby Lobby wasn’t paved by the Christian Right. It was the Catholic Church, more specifically the U.S. Catholic bishops’ conference, that largely engineered Hobby Lobby to block the legitimization of contraception as a standard health insurance benefit—a last ditch effort to prevent by law what it couldn’t prevent from the pulpit: women from using birth control.

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The Catholic bishops’ interest in “conscience clauses” that would allow employers to opt out of reproductive health care services began in earnest in the late 1990s, with the increased viability at the state and national levels of contraceptive equity measures designed to ensure that health plans covered prescription contraceptives like the Pill just like other prescription medications. For years, insurers had omitted contraceptives from prescription drug plans—the only entire class of drugs routinely and explicitly excluded—which made women’s out-of-pocket medical expenses some 70 percent higher than men’s. Measures to ensure contraceptive equity had been stalled by male legislators and social conservatives who asserted that employers and insurers shouldn’t be forced to pay for what they called a “lifestyle” choice, not a health care need. Despite that fact that nearly all women use contraceptives at some point in their lives—98 percent, according to government surveys—and that at any given moment two-thirds of women of child-bearing age are using a contraceptive method, the implication was that fertility management was frivolous or immoral and that “other people” shouldn’t be forced to pay for it.

When Connecticut considered a contraceptive equity measure in 1999, a Catholic priest, the Rev. Joseph Looney of Bethlehem, Connecticut, told the legislature that covering contraceptives would only benefit “playboys” and would fund “craziness and irresponsibility.” It was a framework that conservatives had successfully applied to abortion—asserting that it must be segregated from other health services and government funding because it was immoral—and now were trying to apply to birth control.

But the decision of most health insurers to cover Viagra almost immediately after it was approved by the FDA in 1998 largely negated this argument. Suddenly contraceptive coverage measures were sailing through state legislatures. A national contraceptive equity measure was introduced but failed to make it out of committee. The sponsors retooled the bill and reintroduced it as a measure that required insurance plans participating in the health insurance program for federal employees to cover contraceptives. Even this scaled-down measure would set an important precedent because the federal benefits package is often used as a model for private sector health plans. The bishops and social conservatives worked furiously to derail the measure by claiming that it would force health plans to cover abortifacients—which they now defined as anything that worked post-fertilization. Representatives Christopher Smith (R-NJ), who had a track record of introducing legislation favored by the U.S. Conference of Catholic Bishops (USCCB), and Tom Coburn (R-OK) tried unsuccessfully to insert a provision prohibiting “coverage for abortifacients,” claiming that newly approved emergency contraceptive pills and the intrauterine device were abortifacients because they could prevent a fertilized egg from implanting.

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When charges that contraceptives were abortifacients failed to halt the measure, the bishops turned to a new tack: claiming that contraception equity laws violated the religious freedom of insurers and employers who disapproved of contraception and would be forced to subsidize its use. “They force private health insurance plans and/or employers . . . to cover all ‘FDA-approved’ methods of contraception. . . regardless of the provider’s conscientious objection or long-standing religious beliefs against such coverage,” wrote Cathy Deeds of the NCCB. It was a stunning claim, suggesting that anyone who administered or paid for an insurance policy should be free to dictate what coverage was provided to policyholders based on their objection to services that they themselves would not be forced to use.

The Catholic bishops now sought a broad-based conscience clause that would allow any employer or insurer to refuse to cover contraceptives for any religious or moral objection. This represented a major escalation in the grounds for claiming conscience protections. Traditionally so-called conscience clauses, like the 1973 Church Amendment, protected individuals or health care entities like hospitals only from being compelled to directly perform abortions or sterilizations in violation of their moral or religious beliefs. In 1997, the federal government expanded conscience protections to the payers of abortion-related services when it allowed Medicaid and Medicare managed-care plans to refuse to pay providers for abortion counseling or referral services. Now the bishops were attempting to extend conscience protection to any payer who had a “moral” objection to contraception. Such a measure would make contraceptive coverage mandates useless, because any employer or insurer could opt out. And it would once again leave women’s reproductive health care at the mercy of individual employers and insurers and stigmatize contraceptives, like abortion, as a segregated health service that could be carved out of the continuum of women’s health needs.

The bishops failed to get a broader conscience clause in the bill mandating coverage of contraceptives for federal employees, but they did manage to get an exemption for the five religiously affiliated plans in the system. Having set the precedent that religious providers would be treated differently concerning the provision of reproductive health care, even in the matter of noncontroversial services such as contraception, the bishops launched a major new effort to create broad conscience exemptions.

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The issue was particularly contentious because the FDA recently had approved the first prepackaged “morning after” pill—a high dose of oral contraceptives that worked to prevent pregnancy if taken shortly after unprotected intercourse. Like regular oral contraceptives, emergency contraceptives (ECs) work primarily by preventing ovulation; however, at the time it was believed that this early version might in some cases prevent implantation. Public health advocates praised the widespread availability of EC as a major step forward in preventing unwanted pregnancy and reducing abortion. The Catholic bishops, however, were among the earliest and sharpest critics of EC, asserting that it was an abortifacient because it may prevent implantation and “destroy a developing embryo” despite the fact that the FDA said it could not interrupt an established pregnancy.

“What is striking is how hard the bishops worked to conflate abortion and contraception, particularly around EC,” said Lois Uttley, director of MergerWatch, which began tracking religiously based health restrictions in the mid-1990s. “But they said it over and over enough that they actually managed to convince many people,” she said.

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During the Bush administration, the Catholic bishops found a willing partner in their quest for “conscience clauses.” President George W. Bush’s PEPFAR anti-AIDS program included an exemption for religious providers who didn’t want to distribute condoms, which was custom-made for Catholic agencies like Catholic Relief Services. Bush signed an appropriations bill in 2005 that included the ﬁrst federal conscience clause. This broadened the abortion exemption to a wide range of health care entities, including HMOs and other insurers, and included the right to refuse to refer for abortions.

By this time, the issue of conscience refusals was becoming increasingly contentious, as the bishops were joined by elements of the Christian Right in asserting the need for greater conscience protections for health care workers, who they charged were regularly being forced to violate their faith in the provision of certain services. Organizations like Pharmacists for Life campaigned for the right of pharmacists to refuse to dispense or refer for oral contraceptives or EC on the grounds that they were potentially abortifacients. Reports of conscience-based service refusals mushroomed. There were hospital nurses who refused to care for patients before or after emergency abortions, doctors who refused to prescribe the Pill to unmarried women, and infertility clinics that turned away lesbian patients. Conscience exemptions were now being used as a political tool to block access to services to which some objected or to make moral judgments about the provision of care to certain patients.

By the dawn of the Obama administration, however, the bishops were losing ground on conscience exemptions. They lobbied unsuccessfully in Arizona to broaden that state’s narrow religious exemption to its contraceptive equity law, which covered only churches, to include any religious employer, such as Catholic hospitals and universities. The bishops in Connecticut lost a bruising two-year battle for an exemption to that state’s new “EC in the ER” law despite putting up a ﬁerce ﬁght. The Obama administration undid some sweeping conscience exemptions created during the Bush administration, noting that federal law still protected providers from being compelled to participate in abortions. Then, in August 2011, the Department of Health and Human Services (HHS) announced that all employer-based health plans would be required to provide contraceptives to women at no cost under its proposed rules for the preventive services guaranteed to all individuals under the Affordable Care Act.

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In deference to the Catholic bishops, HHS proposed a narrow conscience clause that exempted nonproﬁt organizations directly involved in the inculcation of religion that primarily employed individuals of the same religion, like Catholic churches and other houses of worship. However, Catholic-affiliated institutions like universities and hospitals that served the general population and employed non-Catholics would have to provide contraception through their plans. Many of these employers had chosen to self-insure—that is, serve as their own insurers—to circumvent state contraception mandates, but they would be required to comply with federal law.

The type of narrowly drawn conscience clause proposed by the administration had been sanctiﬁed by two closely watched state supreme court decisions in New York and California. The U.S. Supreme Court let both decisions stand, which was seen as a major victory for a limited application of conscience clauses. But in the ensuring years since the 2006 New York decision, not only had the Christian Right become activated on the issue, but the question of conscience clauses had spilled beyond health care as efforts advanced to ensure equality for same-sex couples. Catholic Charities affiliates in Boston and Illinois closed their well-respected adoption agencies rather than comply with state mandates that they provide adoptions to gay and lesbian couples.

Then in September 2011, shortly after the Obama administration announced the contraceptive mandate, HHS announced that it would not renew a contract with the USCCB to provide assistance to victims of international human trafficking because the bishops’ organization refused to provide women who had been subjected to rape or forced prostitution with access to comprehensive reproductive health care, including abortion, EC, and family planning and sexually transmitted disease counseling. Where HHS saw the need to provide all medically appropriate services to these women, the bishops claimed anti-Catholic discrimination, especially because political appointees at HHS had overruled a program evaluation that rated the USCCB as the top-performing contractor in terms of service provision. Sister Mary Ann Walsh, a spokesperson for the USCCB, said that there was a “new, albeit unwritten rule of HHS, the ABC rule—Anybody But Catholics.

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It was a dramatic charge and signaled that the bishops were going to make a full-court press on the issue of exemptions for Catholic providers. In mid-November, USCCB president Archbishop Timothy Dolan of Milwaukee, Wisconsin, announced a new Committee for Religious Liberty to counter what he said was a move to “neuter religion” in the public square. The committee was put under the direction of Bridgeport, Connecticut, Bishop William Lori, an outspoken conservative who was formerly the head of the Pro-Life Committee, and staffed by Anthony Picarello, a rising young lawyer at the USCCB who had worked as a litigator for the Becket Fund for Religious Liberty, which had pursued a number of high-profile religious freedom cases.

In addition to the contraceptive mandate, Dolan named the dropping of the USCCB from the HHS contract, state marriage equality laws that required same-sex couples be allowed to adopt, and the Obama administration’s failure to defend the Defense of Marriage Act, which prohibited federal recognition of same-sex partnerships, as government actions that “infringe upon the right of conscience of people of faith.” The bishops were charging that efforts to make them play by the same rules as other health and social service providers were affronts to religious freedom—their freedom to discriminate against others or deny services in the name of religion.

There was more at stake that just the bishops’ authority over services provided by Catholic institutions. Domestic and international social service agencies affiliated with the church, like Catholic Charities USA and Catholic Relief Services, receive hundreds of millions of dollars in government contracts each year to provide social services to the poor, run adoption agencies, and manage international development projects. Catholic Charities affiliates received nearly $3 billion in government funding in 2010, accounting for more than 60 percent of their revenue. Religiously affiliated hospitals in the United States, of which 70 percent are Catholic, receive some $40 billion in government funding each year through Medicare and Medicaid and other government programs.

The bishops were making the preservation of their right to participate in these federally funded programs and discriminate based on religious doctrine their most high-profile crusade since Roe v. Wade. Between the launch of the religious freedom committee and the election of Dolan, who was selected over the organization’s more moderate vice president, the bishops were trying to reclaim the national leadership role on social issues that they had enjoyed under pugnacious, outspoken conservatives like the late Cardinal John O’Connor.

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With the bishops’ newly aggressive stance, all eyes turned to the White House to see if Obama would accept the HHS rule, with its narrow conscience exemption, or seek to pacify the increasingly outspoken bishops. He came under ferocious lobbying from the reproductive rights community to maintain the mandate after a private meeting with Dolan at the White House that left the archbishop “feeling a bit more at peace about this issue,” which many took to mean that he had received assurances from Obama that he would soften the mandate.

But no one was prepared for the firestorm that broke loose when the mandate, with its narrow religious exemption intact, was announced on January 20. That the bishops screamed bloody murder shouldn’t have come as any surprise. They had announced their intention to make this their defining issue. But the mandate was also denounced by Sister Keehan, who had proved such a critical ally to the White House on the health reform bill, and a handful of mostly male, liberal-leaning Catholic columnists and pundits, who seemed to think the administration was asking nuns in habits to stand on street corners handing out condoms rather than proposing a reasonable compromise on the issue that had been affirmed by two influential high courts. Also lost in the debate was the fact that many Catholic health plans like the OSF Health Plan in Illinois already routinely covered birth control through a third-party administrator, an arrangement that proved adequate for these plans for at least a decade.

The Obama administration announced that religiously affiliated employers would be given an additional year to figure out how to apply the mandate, but that didn’t mollify the bishops, who contended that the mandate was an affront to rank-and-file Catholics—even though some 98 percent of Catholic women have used birth control and nearly 60 percent of all Catholics supported the mandate. In addition, many of the 650,000 employees of Catholic hospitals aren’t Catholic, which meant that the bishops had absolutely no moral authority over their reproductive health choices. Dolan argued in a video made even before the administration released the final rule, however, that the mandate was a violation of religious freedom because it would force Catholics “to go out into the marketplace and buy a product that violates their conscience.”

It was a radical new way of viewing conscience rights—not as the right of an individual to decline to use or participate in a service, but as their right to deny that service to others based on their mere participation in an insurance pool in a commercial marketplace.

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But with Catholic use of birth control nearly universal, Dolan needed to raise the stakes. He drew on years of efforts by the bishops to conflate abortion and contraception, and particularly abortion and emergency contraception, to charge that the mandate would require Catholic insurers and employers to cover “abortion-inducing drugs” in a reference to EC. He made the charge even though the official journal of the Catholic Health Association had published an article nearly two years earlier saying that Plan B, the most widely used emergency contraceptive, was not an abortifacient—even under the bishops’ definition—because it worked to prevent fertilization, not implantation. The general medical community also was increasingly in agreement that post-fertilization effects of EC were virtually nonexistent.

But no sooner had all the parties breathed a sigh of relief than the bishops backtracked and denounced the compromise, saying Catholics were still “being called upon to subsidize something we find morally illicit.” It was a rehash of the bishops’ long-running contention that funding streams could never be adequately segregated in the case of morally illicit services, but now they were applying it to birth control. Conservative Catholics like Robert George and Mary Ann Glendon took up the bishops’ tack and called the compromise a “cheap accounting trick.” But many Catholic moral theologians disagreed, saying that Catholic institutions’ role in the provision of contraception under the compromise would be remote material cooperation, which was acceptable and widely used in the realm of health care to allow Catholic hospitals to operate in secular society.

But the bishops wouldn’t back down. Instead, they took their demands one step further, calling for a broad conscience clause that would allow any employer who had a moral objection to contraception to refuse to provide it. Increasingly it looked as if the fight wasn’t about finding a reasonable compromise that would allow Catholic employers to distance themselves sufficiently from the provision of contraception to satisfy at least the letter of the widely ignored Catholic teaching on contraception. It was an attempt to block the federal enshrinement of contraception as a basic women’s health care right.

The full scope of the issue didn’t become apparent to most people until a few days later, when the Republican-run House Committee on Oversight and Government Reform held a hearing on the mandate and its supposed impediment to religious freedom. Within hours a picture from the first panel of witnesses was ricocheting around the Internet and social media sites like Twitter. It showed five middle-aged men—half in clerical garb— testifying about women’s access to birth control. There was Bishop Lori, testifying for the USCCB; the Reverend Matthew Harrison, president of the Missouri Synod of the Lutheran Church, a conservative Lutheran sect that has long been prominent in the anti-abortion movement; Meir Soloveichik, a conservative rabbi; and two conservative Christian theologians. When Georgetown University law student Sandra Fluke, a non-Catholic whose student health insurance excluded contraception, was denied the right to testify on the basis that the hearing wasn’t about women’s access to birth control but religious freedom, the picture became clear to many for the first time.

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Women’s health advocates and political pundits expressed amazement that contraception could be so controversial in 2012. But they shouldn’t have been surprised. That’s because the forty-year fight over reproductive rights had never really been about abortion; it had always been about women and sex—specifically, the ability of women to have sex without the consequence of pregnancy. That’s why it was the shot heard ’round the world when in the midst of the flap over the all-male birth control panel radio talk show host Rush Limbaugh called Fluke a “slut” for wanting her insurance to treat birth control like any other prescription medication. Limbaugh had revealed what the right really believed about women and sex: Women who wanted to have sex—especially outside of marriage— and control their fertility were doing something fundamentally illicit and shouldn’t expect anyone else to pay for it. To them, birth control was just a lesser form of abortion.

Adapted from "Good Catholics: The Battle Over Abortion in the Catholic Church" by Patricia Miller. (University of California Press, 2014)