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The Supreme Court on Wednesday handed the Little Sisters of the Poor, a group of Catholic nuns that cares for impoverished elderly people, a major victory in their ongoing legal ordeal over a mandate in the Affordable Care Act (ACA) that required them to pay for contraceptives in their health care coverage.

The court, in an opinion written by Justice Clarence Thomas, judged that a Trump administration rule that provided an exception to the mandate for religiously-affiliated groups and some for-profit companies was legal -- leading many on the right to declare final triumph for the Little Sisters after years of litigation.

"VICTORY AT LAST!" tweeted Rep. Jody Hice, R-Ga.

SUPREME COURT RULES IN FAVOR OF LITTLE SISTERS OF THE POOR IN OBAMACARE CONTRACEPTION CASE

The Trump campaign pointed fingers at Obama-era Vice President Joe Biden, the Democrats' presumptive 2020 presidential nominee. "Joe Biden's decade-long war against Catholic nuns and the Little Sisters of the Poor is finally over. Today's Supreme Court ruling is a landmark win for religious liberty. Unlike Joe Biden, President Trump has been a staunch defender of religious freedom since taking office and will always fight to defend communities of faith," Trump 2020 Deputy Communications Director Ali Pardo said.

Judicial Crisis Network Vice President and Senior Counsel Frank Scaturro explained on Twitter: "The Court’s decision today upholding that exemption is a victory for freedom of religion and conscience—for the Little Sisters and for everyone. Let’s be thankful that the Little Sisters’ ordeal in court has finally ended."

But two concurring opinions -- one authored by Justice Samuel Alito and another by Justice Elena Kagan -- signal that the two states involved in the litigation, Pennsylvania and New Jersey, may bring the nuns back to court again.

Alito's opinion was joined by Justice Neil Gorsuch, while Kagan's was joined by Justice Stephen Breyer.

Both indicated they agreed with the majority's ruling that the Trump administration had the authority to exempt the Little Sisters and other similar groups from the contraceptive mandate. But Kagan's opinion expressed suspicion of the Trump administration's motivations when it implemented the rule, while Alito's lamented that Thomas' majority opinion didn't go further to foreclose the kind of administrative law challenge Kagan alluded to.

Justices Samuel Alito and Elena Kagan seemed to indicate Wednesday that the Little Sisters of the Poor's legal saga may continue.

Justices Samuel Alito and Elena Kagan seemed to indicate Wednesday that the Little Sisters of the Poor's legal saga may continue.

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"I also write separately because I question whether the exemptions can survive administrative law’s demand for reasoned decisionmaking. That issue remains open for the lower courts to address," Kagan said in an opinion.

"But that does not mean the Departments should prevail when these cases return to the lower courts. The States challenged the exemptions not only as outside [the Health Resources and Services Administration]'s statutory authority, but also as 'arbitrary [and] capricious,'" she said. "Because the courts below found for the States on the first question, they declined to reach the second. That issue is now ready for resolution, unaffected by today’s decision. An agency acting within its sphere of delegated authority can of course flunk the test of 'reasoned decisionmaking.'"

Alito appeared all but sure that Pennsylvania and New Jersey would take Kagan up on her invitation.

'An agency acting within its sphere of delegated authority can of course flunk the test of 'reasoned decisionmaking.''

— Justice Elena Kagan

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"We now send these cases back to the lower courts, where the Commonwealth of Pennsylvania and the State of New Jersey are all but certain to pursue their argument that the current rule is flawed on yet another ground, namely, that it is arbitrary and capricious and thus violates the APA," he wrote. "This will prolong the legal battle in which the Little Sisters have now been engaged for seven years—even though during all this time no employee of the Little Sisters has come forward with an objection to the Little Sisters’ conduct."

He added that the court should have decided whether the Religious Freedom Restoration Act (RFRA) in fact requires an exemption like the one granted by the Trump administration, because if so, "the Departments did not act in an arbitrary and capricious manner in granting it."

Alito said: "And in my judgment, RFRA compels an exemption for the Little Sisters and any other employer with a similar objection to what has been called the accommodation to the contraceptive mandate."

Judicial Crisis Network's Scaturro noted that if the states continue to push the case against the nuns, they would be burning taxpayer money on a challenge that he said is unlikely to succeed.

"If Pennsylvania and New Jersey were to try to protract this litigation with an arbitrary and capricious challenge to the Little Sisters’ conscience protection, it would show hubris and waste their taxpayer dollars," Scaturro told Fox News. "After all, they were just told by the Court that the administration had the statutory authority to adopt the rule, and the justices rejected their attempt to add a test about the agencies’ 'open-mindedness' in a procedural challenge to the rule."

'I would bring the Little Sisters’ legal odyssey to an end.'

— Justice Samuel Alito

Kagan, however, said that the rule was overbroad and that she thinks it would be a "close call" if it could stand.

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Alito harbored none of Kagan's concerns, however, and said that the RFRA, which states that unless it meets a strict test, "the Federal Government may not 'substantially burden a person’s exercise of religion even if the burden results from a rule of general applicability,'" forces the government to carve out an exemption to the contraception mandate.

"I would hold not only that it was appropriate for the Departments to consider RFRA, but also that the Departments were required by RFRA to create the religious exemption (or something very close to it)," Alito wrote. "I would bring the Little Sisters’ legal odyssey to an end."

Fox News' Kristina Biddle contributed to this report.