Several states sued the federal government, and multiple Circuit Courts placed injunctions on the new rules as arbitrary and capricious and required by neither the ACA or the RFRA, violating the Administrative Procedure Act (APA).

The ACA did not displace the system then in effect whereby most of the U.S. population receives health insurance under plans that their employers arrange through the private market.

[3][4] Numerous religious groups, both for- and nonprofit and particularly those of the Catholic faith, were critical of the mandate, arguing that the use of contraceptives is morally wrong and a sin.

[1] The Christian-based retail franchise Hobby Lobby argued that the mandate violated its free exercise of religion rights established by the First Amendment of the United States Constitution and affirmed in the Religious Freedom Restoration Act (RFRA).

[2] Before Zubik was heard in oral arguments, Justice Antonin Scalia died, and as he had joined the majority in Hobby Lobby, the possibility of a tie vote arose.

In May 2017, Trump enacted Executive Order 13798, "Promoting Free Speech and Religious Liberty", which directed HHS to consider alternate routes to address conscience-based objection[7] and led HHS to issue new interim rules that allowed employers with religious or moral objections to be exempted from ACA's contraceptive mandate.

Among the first was Pennsylvania; later, New Jersey challenged the Government in the United States District Court for the Eastern District of Pennsylvania, asserting that the process violated the Administrative Procedure Act (APA), Title VII of the Civil Rights Act of 1964, and the Equal Protection Clause of the Fourteenth Amendment and the Establishment Clause of the First Amendment of the Constitution.

[11] Despite the federal government's and the Supreme Court's efforts to resolve the issue, several Catholic groups, including the Little Sisters, denied that any accommodation had been made at all.

"[12] Citing the same moral theory, the Sisters' co-litigants Priests for Life held that filing out the government paperwork (Form 700) would not only register their objections and exempt them from participation in the plan but would also trigger a series of events that in the end would result in the delivery of contraception to persons in their employ who sought it.

Their brief to the Court stated that this would cause "mortal sin and scandal" and that "This is true whether the immoral services are paid for directly, indirectly, or even not at all by Priests for Life.

"[13] Covering the controversy for Roll Call, Melinda Henneberger wrote, "Religious nonprofits can be exempted if they sign a form notifying the government, which then sets up the coverage through the group's existing plan at no additional cost to the organization.

"[14] She put the matter to the Witherspoon Institute’s Matthew J. Frank, who responded that for the Catholic groups in the case, "signing the form is the violation of the faith.

"[15] They conclude that in line with Catholic tradition the Sisters "very reasonably conclude that compliance with the Mandate—whether by executing Form 700, by submitting the HHS Notice, or by maintaining a health plan or insurance relationship through which the objectionable coverage is provided—would involve either formal cooperation in wrongdoing, or impermissible material cooperation in serious wrongdoing, and would therefore be gravely wrongful.

"[17][4] Those opposing the mandate held that what constituted a "substantial burden" under RFRA should be determined by the religious party involved, not the government.

…[this] assertion of authority over the question of what is a substantial burden contradicts founding principles, the First Amendment, RFRA and this Court's precedents.

"[19] The Third Circuit court had agreed with the government's position that thanks to the accommodation any sense of responsibility by the religious objectors should be settled: "The religious objectors who oppose the Accommodation mechanism disapprove of 'what follows from' filing the self-certification form[,] …[but] 'the actual provision of contraception coverage is by a third party,' so any possible burden from the notification procedure is not substantial.

"[20] The Supreme Court held that the government had dodged "the question that RFRA presents (whether the HHS mandate imposes a substantial burden on the ability of the objecting parties to conduct business in accordance with their religious beliefs)" and had arrogated "the authority to provide a binding national answer to this religious and philosophical question...namely, the circumstances under which it is wrong for a person to perform an act that is innocent in itself but that has the effect of enabling or facilitating the commission of an immoral act by another.

[19] FLI argued that as "the Accommodation also require the religious employers who object to it to violate their beliefs or incur a penalty for noncompliance", the Sisters would refuse to comply with the accommodation and face the same heavy monetary penalties for resisting regulations that violate their religious convictions as the owners of Hobby Lobby faced.

[18] FLI also dismissed the Third Circuit's claim that the effect on non-religious parties for enforcing RFRA had to be weighed in any decision invoking it.

The Court had worried that finding for the religious objectors "would impose an undue burden on nonbeneficiaries—the female employees who will lose coverage for contraceptive care.

Reese pointed out that shortly before the controversy began the HHS had denied the U.S. Conference of Catholic Bishops a government grant to assist people being trafficked on account of their refusal to refer clients for birth control or abortion services.

"[12] Reese reported that there were also those around Obama who held that the conflict with the bishops would rally their own base as well, including supporters of Planned Parenthood (which opposed all exemptions).

Thomas wrote that "We hold that the [administration] had the authority to provide exemptions from the regulatory contraceptive requirements for employers with religious and conscientious objections.