Justice Samuel Alito leaves the stage after speaking at the Federalist Society's National Lawyers Convention in Washington on Nov. 17. (Cliff Owen/AP)

Justice Samuel A. Alito Jr. on Thursday said free speech and religious liberty hang in the balance at the Supreme Court and warned of other issues along the “constitutional fault lines” that might confront the divided justices.

A little more than a week ago, it seemed those issues would come before a court with a liberal majority for the first time in nearly half a century. Instead, the election of Donald Trump is likely to mean a restoration of the conservative majority that prevailed before the death of Justice Antonin Scalia in February.

In a speech before the conservative Federalist Society’s National Lawyers Convention, Alito did not mention the election or the vacancy on the court. But he listed the issues that concern him, including gun rights and alleged overreach by government agencies, and said they should be answered with this thought in mind: “What would Scalia do?”

That is pretty much the theme of the three-day conference that opened Thursday. Scalia was an early supporter of the Federalist Society, which supports a conservative view of the Constitution and has been an active participant in advising Republican presidents on filling the federal judiciary.

The society, along with the Heritage Foundation, helped produce a list of potential nominees from which Trump says he will make his Supreme Court choice. Nine of the 21 people on the list have been participating in the conference.

The mood was jovial. An organization that has been on defense for the past eight years — a home to those mounting legal challenges to President Obama’s policies — is ready to play offense again.

Alito steered clear of any direct mention of that. But he noted that some of the issues that most concerned him were decided by 5-to-4 majorities and said the “constitutional fault lines” were dangerous places.

“Sometimes the earth starts to tremor and people get worried about what’s coming,” Alito said.

In District of Columbia v. Heller, for instance, the court decided in 2008 that “the Second Amendment actually means what it says,” Alito said, and protects an individual right to own a firearm for self-defense. But Justice Stephen G. Breyer’s dissent in the case “provides a road map for denaturing Heller without actually overruling it,” Alito said.

Likewise, Alito said he was alarmed that more than 40 senators were willing to amend the Constitution to overturn the court’s ruling in Citizens United v. FEC, which held that restrictions on corporate and union political spending violated free-speech rights.

“What would that amendment do?” Alito said. “It would have the effect of granting greater free-speech rights to an elite group — those who control the media — than to everybody else.”

Religious freedoms, Alito said, are “in even greater danger.” Quoting “the latest recipient of the Nobel Prize for literature,” Bob Dylan, Alito said, “It’s not dark yet, but its getting there.”

Alito objected to the court’s decision in June not to review a requirement in the state of Washington that pharmacies dispense emergency contraceptives to women. It was challenged by pharmacists who said that they considered some of the drugs to be tantamount to abortion and that dispensing them violated their religious beliefs.

Alito said he missed Scalia in ways that transcend the court’s jurisprudence. In the court’s arguments and conferences since February, Alito said, “there has been a palpable emptiness in the room. Something vital is obviously missing.”

After speaking to the Federalist Society chapter at Columbia University, Alito said, he was given a T-shirt that read “WWSD,” a play on the popular Christian slogan “What would Jesus do?

“At the time, it struck me as slightly sacrilegious,” Alito said, adding, “Now the question is real.”