There’s a vacancy on the bench and a prohibition on in-person arguments, but the Supreme Court’s new term began Monday and the court is already making waves.

The court left in place a decision that allowed a lawsuit to move forward against a Kentucky clerk who was jailed in 2015 after refusing to issue marriage licenses to same-sex couples.

The high court said Monday it would not take the case involving Kim Davis, the former clerk of Rowan County, and two same-sex couples who had sued her. Soon after the 2015 Supreme Court decision in which same-sex couples won the right to marry nationwide, Davis, a Christian who has a religious objection to same-sex marriage, stopped issuing all marriage licenses.

That led to lawsuits against her, and a judge ordered Davis to issue the licenses. She spent five days in jail after refusing.

Supreme Court justice Clarence Thomas wrote for himself and Justice Samuel Alito that while he agreed with the decision not to hear the case, it was a "stark reminder of the consequences" of the court's 2015 decision in the same-sex marriage case in Obergefell v. Hodges.

Because of that case, he wrote, “those with sincerely held religious beliefs concerning marriage will find it increasingly difficult to participate in society without running afoul" of the case “and its effect on other antidiscrimination laws.”

Of Davis, Thomas and Alito said she was being persecuted for her "traditional Christian values."

"Davis may have been one of the first victims of this Court’s cavalier treatment of religion in its Obergefell decision, but she will not be the last," they wrote.

It appears the Justices are taking aim at Obergefell v. Hodges – and with Senators working to confirm a possible Conservative justice, that has some advocates worried for the future of same-sex marriage.

They also declined to hear Skidmore v. Led Zeppelin, a copyright dispute over the iconic song "Stairway to Heaven."

Chief Justice John Roberts opened up the session with a tribute to the late Justice Ruth Bader Ginsburg, saying "During her time on the court, she authored 483 majority, concurring and dissenting opinions. Justice Ginsburg’s contributions as an advocate, jurist and citizen are immeasurable."

The list of cases the court may hear this term includes a lawsuit over the future of the Affordable Care Act. Texas v. California revisits the issue over whether Congress has the constitutional authority to regulate the insurance market.

In 2012, Chief Justice John Roberts joined the four liberal justices in saying it did because the individual mandate included a financial penalty, and Congress has the power to levy taxes.

But there’s been a big change since then.

"The question is if the tax penalty is zeroed out, which is what the Trump tax legislation did,” asks law professor Maya Manian, “then are there still constitutional grounds for upholding the Affordable Care Act?"

Manian says the stakes are high.

"It could provide an opportunity to simply say the whole law must be struck down and that would have huge implications on access to health care, especially while we are in the middle of a pandemic,” she added.  

In addition to the individual mandate, the ACA also includes an expansion of Medicaid, coverage requirements for people with pre-existing conditions, and other measures to increase access to health insurance. But even if the justices agrees the tax law changes mean the 2012 decision is no longer relevant, they could also issue a narrower ruling, throwing out part of the law but allowing the rest to stand.

Arguments in the case are set for November 10, but what is not clear yet is whether the seat left vacant by the death of Justice Ruth Bader Ginsburg will be filled before then.

President Donald Trump wants his nominee Amy Coney Barrett confirmed as soon as possible, which could tip the balance of the court.

“She does have some writings where she was critical of Chief Justice Roberts decision to uphold the Affordable Care Act,” says Manian.

In a 2017 Notre Dame Law School article, Barrett criticized Chief Justice John Roberts' reasoning to uphold the Affordable Care Act, saing that he "pushed the Affordable Care Act beyond its plausible meaning to save the statute."

Democrats have zeroed in on the future of the Affordable Care Act, which is colloquially referred to as "Obamacare," in their opposition to Barrett's nomination.

Speaking the day after she was nominated, Democratic presidential candidate Joe Biden said Barrett has a "written track record of disagreeing adamantly with the Supreme Court's decisions on two occasions upholding the ACA."

The ACA has been challenged in the Supreme Court multiple times, and was prominently featured in two major cases: National Federation of Independent Business v. Sebelius (2012) and Burwell v. Hobby Lobby Stores, Inc. (2014).

There’s a political fight brewing over whether Barrett should be confirmed before the presidential election, in part because the court could get involved if there’s a dispute over the election results.

"Certainly President Trump is setting the setting the stage for that already by already claiming without evidence that absentee ballots and mailing ballots will be fraudulent," explains Manian. 

Twenty years ago, the election did come down to a Supreme Court ruling Bush v Gore.  Five justices ruled that Florida should stop its recount, and since George W. Bush was ahead at the time, he won Florida’s electoral votes and, ultimately, the presidency.

The Supreme Court can hear arguments and issues rulings without nine justices present, but the nation's highest court also has the option to re-hear arguments once the vacancy is filled as long no decision has been issued.

The deadline for those decisions is the end of the term in June.