After revelations of Fani T. Willis’s romance with a subordinate sent the Georgia criminal case against Donald J. Trump down a two-month detour worthy of a soap opera, a judge’s ruling on Friday resolved a major cliffhanger. Ms. Willis could continue prosecuting the case, so long as her ex-boyfriend withdrew from it.

But the resignation hours later of the former boyfriend, Nathan J. Wade, whom Ms. Willis hired as a special prosector, only settled so much. A fresh and complicated array of problems lies ahead for Ms. Willis, and for one of the most significant state criminal cases in American history.

“Her troubles are far from over,” Clark D. Cunningham, a law professor and ethics specialist at Georgia State University, said in an email on Friday.

The defense effort to disqualify Ms. Willis began in early January, upending the case and making it unlikely to reach trial before the November rematch between Mr. Trump and President Biden. Any attempts to appeal Friday’s ruling by Judge Scott McAfee of Fulton County Superior Court could delay matters even further.

Republicans have smelled blood. The G.O.P. lawmakers who dominate Georgia politics have created new ways to investigate Ms. Willis, which could potentially lead to her removal from office. And last week, a young lawyer named Courtney Kramer, a former intern in the Trump White House, announced that she would run against Ms. Willis in this year’s race for district attorney.

Ms. Kramer’s campaign, while unlikely to succeed in heavily Democratic Fulton County, could amplify criticism of Ms. Willis and the case, which charges Mr. Trump and some of his allies with conspiring to overturn his 2020 election loss in Georgia.

Mr. Trump has made Ms. Willis’s troubles a recurring talking point at rallies. One of his staunchest allies in Congress, Representative Jim Jordan, is chair of the House Judiciary committee, which has been investigating Ms. Willis and her prosecution of the former president. On Thursday, Mr. Jordan sent a letter to Ms. Willis threatening to invoke contempt of Congress proceedings against her if she did not turn over certain documents related to her office’s use of federal funds.

All of these attacks could help to sow doubts about the district attorney and her case in the minds of future jurors.

As the pressure has mounted, Ms. Willis has responded with fierce defiance. Soon after news of the relationship broke, she gave a speech at a Black church in Atlanta, calling herself “flawed, hardheaded and imperfect” but also suggesting that her critics were motivated by racism.

Just last week, at an International Women’s Day event, she lashed out against “idiots” who criticized her and mispronounced her name as “Fanny” — it’s FAH-nee — and recounted how a friend had recently asked if she regretted becoming district attorney.

“Are you kidding?” Ms. Willis recalled responding. “I’m the best D.A. this county’s ever had.”

Mr. Cunningham said that even after Friday’s ruling, Ms. Willis and her entire office could still be removed from the case if an appeal were to succeed, which would send it skidding into new realms of uncertainty and potential chaos. The judge, he noted, pointed to lingering questions about whether Ms. Willis and Mr. Wade “testified untruthfully,” even saying in his ruling that “an odor of mendacity remains.”

“Trump and his co-defendants will surely appeal,” Mr. Cunningham said in his email, “and Judge McAfee’s order gives plenty of basis for them to argue to the court of appeals that just removing Wade is an inadequate remedy.”

It is not clear how much Mr. Wade’s resignation sets back the case. Ms. Willis has described him as a longtime trusted ally. And as the manager of the Trump prosecution team since November 2021, he possesses a wealth of institutional knowledge that would have been particularly helpful if the case stretches out for months, or even years.

At the same time, there is no evidence that Mr. Wade, a lawyer and former municipal court judge from the Atlanta suburbs, ever handled a major political corruption case before Ms. Willis hired him. Indeed, his scant experience was a key argument in the original motion to disqualify Ms. Willis.

Ashleigh Merchant, the defense lawyer who filed the motion, claimed that Ms. Willis had hired an underqualified boyfriend, paid him handsomely from public coffers, and then benefited from vacations that she and Mr. Wade took together.

A more serious problem for Ms. Willis and the case may lie in the new state commission that has the power to investigate and remove elected prosecutors.

The commission, made up of Republican appointees, was created last year but was stymied by legal problems that the legislature addressed in a recent measure. It is likely to face a court challenge before it can begin its work.

A second group made up of mostly Republican state senators and dedicated to investigating Ms. Willis has already begun holding hearings. Its leader, Senator Bill Cowsert, has said that the group does not want to conduct a “witch hunt.” But it has the power to subpoena documents and witnesses, and it called Ms. Merchant as its first witness last week.

Before Ms. Merchant’s motion to disqualify Ms. Willis, the prosecution had secured pleas from four of the original 19 defendants in the sprawling racketeering case. Presumably, any talk of additional deals shut down as defendants waited to see whether Ms. Willis and her office would be thrown off the case. It is unclear whether the events of the last two months will make further plea talks less likely.

The best news for Ms. Willis on Friday was that Judge McAfee declined to force her off the Trump case. But she also scored smaller victories, as the judge declined to punish her for other actions. Among them was the speech she gave at the church.

Steven H. Sadow, the main lawyer for Mr. Trump in Georgia, had described the speech as “provocative and inflammatory extrajudicial racial comments” meant to “publicly denounce and rebuke the defendants.” He argued that they were troubling enough to disqualify Ms. Willis and her office and dismiss the indictment.

Judge McAfee declined to go that far, although he did call Ms. Willis’s statements “legally improper.” And he suggested that he was open to issuing a gag order that would block Ms. Willis from mentioning the case in public from now on.

But does keeping Ms. Willis quiet help or hurt the case as it drags on? Much like Mr. Trump, she does not shy away from the spotlight. And like Mr. Trump, her talkative, combative nature has won her enthusiastic fans.

In December, a few weeks before the relationship was brought to light, Ms. Willis drew applause and cheers as she spoke at an event in New York honoring her.

“A lot of folks mad,” she said, “But I’m still here.”