In a lawsuit filed in a state court late Wednesday, Mr. Moore, who denied the allegations of sexual impropriety, complained that pervasive fraud had tainted the election, and that the Alabama authorities had inadequately investigated potential misconduct.
But Mr. Moore found himself aligned against Democrats and Republicans alike. Secretary of State John H. Merrill, a Republican who voted for Mr. Moore, said he had found no evidence of endemic fraud and refused to postpone certification proceedings. Judge Johnny Hardwick of Montgomery County Circuit Court, citing a lack of jurisdiction, dismissed Mr. Moore’s complaint minutes before the vote was certified.
Mr. Jones’s transition team said in a statement that the lawsuit was “a desperate attempt by Roy Moore to subvert the will of the people.”
“The election is over,” the statement added, “it’s time to move on.”
Although the state ultimately certified the results, Mr. Moore’s litigation infused a strain of drama into a day that Alabama officials had hoped would be procedural and perfunctory. Mr. Moore’s lawsuit was late in coming: His lawyers filed their lawsuit at 10:33 p.m. on Wednesday. .
Yet the complaint by Mr. Moore, a figure with a penchant for last-minute legal theatrics, was not altogether surprising. He and his allies have spent the last several weeks signaling their unease with the voting process, and, while saying little else publicly, Mr. Moore solicited contributions for an “election integrity fund.”
Until Wednesday night, it was not clear what would come of his efforts. Then, in a court filing that ran for dozens of pages, Mr. Moore argued that returns in the state’s most populous county “confirmed election fraud.” It also said that turnout in the county was suspiciously high; it suggested that Mr. Jones had benefited from voter intimidation; and it argued that Mr. Moore’s opponents had spread “lies and fraudulent misrepresentations.”
To support his arguments, Mr. Moore included affidavits from several people his campaign described as experts in elections; one has claimed to have “mathematically proved a conspiracy to assassinate” President John F. Kennedy. (Mr. Moore has himself indulged in conspiracy theories, including that former President Barack Obama was not born in the United States.)
Experts unaffiliated with either the Jones or Moore campaigns quickly said the lawsuit’s arguments appeared meritless.
“It seems to boil down to: I should have won under the exit poll and all of this voting by African-Americans must show fraud,” Richard L. Hasen, an elections law expert at the University of California, Irvine, wrote on his blog.
Although the Alabama Republican Party, and many elected officials, stood behind Mr. Moore during his campaign, he had few influential allies by the time the certification meeting began at the Capitol. Party leaders, including President Trump, who endorsed Mr. Moore, had called for him to concede.
Mr. Moore could conceivably ask the Senate, which has the constitutional authority to serve as “judge of the elections, returns and qualifications of its own members,” not to seat Mr. Jones. Republican leaders in Washington are unlikely to heed any such call.
But the final tally reflects Mr. Moore’s enduring appeal to many Republicans here, and Mr. Moore’s strength, diminished as it is, has fueled speculation about whether he will unsettle the state’s politics next year.
A campaign for either governor or attorney general would involve challenging a Republican incumbent and would test just how weary and wary the party is of Mr. Moore.
“On paper, he would be competitive in a Republican primary,” said State Auditor Jim Zeigler, a Republican who supported Mr. Moore in the Senate election and is himself considering a run for governor. “But the campaign is not won or lost on paper, just like a football game. On paper, Alabama was going to beat Auburn, and it didn’t happen.”
The political math for Mr. Moore is certainly more complicated than ever before.
He was twice elected — and effectively twice removed — as chief justice, and he would enter any 2018 race with some of the advantages that can come with decades in public life: name recognition and, likely, the sustained fealty of the devoted supporters who helped him earn more than 650,000 votes on Dec. 12.
But before the Senate race, many of Mr. Moore’s critics regarded him as bigot and a demagogue who cheered discrimination against gay people and Muslims. After the campaign, some of his critics also saw him as a predator toward younger women. And the coalition that sunk Mr. Moore’s campaign — young people, women and black voters in major cities and rural counties — has not gone away.
If Mr. Moore harbors any ambitions of moving into the neoclassical Governor’s Mansion, he will have to act on them quickly: The deadline for declaring a statewide candidacy is Feb. 9.
Several of Mr. Moore’s advisers, including his campaign’s chairman and treasurer, did not respond to messages this week. But a former chief of staff to Mr. Moore, Ben Dupré, said that Mr. Moore is “a guy that does not compromise.”
“He doesn’t take his orders from the Republican Party or the Democrat Party,” said Mr. Dupré, who sometimes spoke for Mr. Moore during the campaign but ended his role soon after the election. “He really believes in following the Constitution and in following God and in following what he believes is his duty to God and to the country.”
Mr. Dupré added, “If he has a reason not to concede, he’s not going to concede. He’s got no friends in D.C. — we know that, we knew that going into this — and he’s not trying to play their game of, ‘Oh, we smeared your reputation, so you should roll over and go away.’”
Mr. Dupré, who spoke hours before Mr. Moore brought his lawsuit, may have a point.
After Mr. Moore faltered in 2006, a political scientist predicted to an Alabama newspaper that it would be “very hard for him to come back and be a major force in Alabama politics.”
Less than seven years later, Mr. Moore, already ousted once from the Supreme Court, was elected chief justice — again.
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