No, she replied, it would take her a few more days.

Mr. Clark, believing that they were on the brink of a deal, flew back to New York.

Outcry on Capitol Hill

But on Capitol Hill, the efforts to upend a resolution were gaining momentum.

While Mr. Weiss concluded that there was not enough evidence to charge Mr. Biden with major crimes, not all his colleagues shared that opinion. The perception that Mr. Biden was being treated too softly spurred resistance among some investigators who believed that his office had blocked them from following all leads.

Few were more frustrated than Gary Shapley. A veteran I.R.S. investigator, he had worked major cases and helped take on big bankers. But every time he said he tried to pursue what he believed could be a major break in the Biden investigation, he felt stymied.

When investigators went to interview Hunter Biden, they were told they couldn’t approach the house. An attempt to serve a search warrant on Joseph R. Biden Jr.’s guesthouse? Denied. The request to search a storage unit belonging to Hunter Biden? Derailed.

Finally, he reached out to Mark Lytle, a former federal prosecutor, and the men eventually connected with former Republican staff members who had worked for Senator Charles E. Grassley, Republican of Iowa, and had knowledge of federal whistle-blower protections.

Mr. Shapley had been raising concerns internally since at least the fall of 2022, but that winter, he took his allegations to the Justice Department’s watchdog, lodging a complaint in February.

By April, Mr. Shapley offered to share insider details with House Republican committee investigators, including his claim that Mr. Weiss had told him that federal prosecutors in Washington and California had refused to bring tax charges against Mr. Biden. His most startling allegation: Mr. Weiss had been so frustrated that he had considered asking Mr. Garland to appoint him as special counsel in late 2022. (Mr. Weiss and Mr. Garland have both denied that account.)

Mr. Shapley requested special protections to bypass legal restrictions on discussing ongoing federal investigations.

It all began to explode into public view on May 15 — the same day Ms. Wolf contacted Mr. Clark — when it was reported that the investigative team that had worked on the case, including Mr. Shapley, had been removed. The next day the chairman of the House Ways and Means Committee fired off a letter to the I.R.S. commissioner demanding an explanation.

Around that time, lawyers for a second tax investigator sent a letter to the I.R.S. commissioner, claiming the team of investigators on the case had been removed after expressing concerns about political interference from the Justice Department.

The letter was quickly made public. The agents’ claims were the breakthrough House Republicans had long been seeking.

The I.R.S. investigators had given Congress something genuinely new: summaries of WhatsApp messages that appeared to show Hunter Biden involved in a shakedown in which he had invoked his father, firsthand testimony from people who had reviewed Mr. Biden’s finances and the credibility of their long careers at the tax agency.

On May 24, CBS aired an interview with one of the agents. Two days later, he testified behind closed doors before the House Ways and Means Committee, creating buzz on Capitol Hill. The second man testified on June 1. Three weeks later, the committee voted to publicly release transcripts of the testimony, leading to even more news coverage.

Shifting Ground

As the testimony from the I.R.S. agents took hold, Mr. Biden’s legal team felt the ground shift beneath them. The U.S. attorney’s office suddenly went quiet.

Early in the negotiations, Ms. Wolf included what seemed like a boilerplate disclaimer in an email, that her team “had not discussed or obtained approval” from her superiors for the terms of the final agreement.

On Tuesday, May 23, after four days of silence, Ms. Wolf delivered unwelcome news. Mr. Weiss had revised what he wanted in the deal, now demanding that Mr. Biden plead guilty to two misdemeanor counts of failing to pay his taxes. It crossed a red line for Mr. Clark.

Erupting in anger, Mr. Clark accused Ms. Wolf of misleading him. He renounced the possibility of any deal, but after consulting with Mr. Biden, reversed course and told Ms. Wolf that Mr. Biden was willing to go along.

Mr. Clark then went to Wilmington to meet the prosecutors, where they hammered out the details of the deal.

By the middle of June, both sides were prepared to announce a deal.

Under the agreement, Mr. Biden would plead guilty to two tax misdemeanors and avert prosecution on the gun charge by enrolling in a diversion program.

Mr. Biden’s legal team was eager to issue a statement claiming that the agreement represented the conclusion of the government’s investigation. That Monday, June 19, Mr. Clark sent a draft to Shannon Hanson, another Weiss deputy, which clearly stated the investigation was over.

“I can confirm that the five-year long, extensive federal investigation into my client, Hunter Biden, has been concluded through agreements with the United States Attorney’s Office for the District of Delaware,” it read.

“With the conclusion of this investigation, he looks forward to continuing his recovery and moving forward,” it continued.

Ms. Hanson suggested the edit from “has been concluded” to “resolved,” and she also asked Mr. Clark to strike the phrase “With the conclusion of this investigation.”

But hours after the agreement was announced, confusion set in. In a news release, Mr. Weiss’s office said that the investigation was “ongoing,” taking Mr. Biden and officials at Justice Department headquarters by surprise.

It was at this critical juncture that Ms. Wolf began to take a significantly reduced role, although it is unclear whether that had anything to do with the Biden case.

In their testimony, the I.R.S. whistle-blowers claimed that Ms. Wolf — who had made a couple of campaign donations to Democrats — had discouraged them from pursuing lines of inquiry that could lead to the elder Mr. Biden.

Around this time, Leo Wise — a senior prosecutor who had spent nearly two decades in the Baltimore U.S. attorney’s office — was quietly transferred to the department’s criminal division, then detailed to Delaware to add legal firepower to the relatively small Delaware office.

It was his name, not Ms. Wolf’s, that appeared on the plea deal. And it was Mr. Wise who was responsible for defending the deal, one he had not negotiated, in front of a federal judge who proved to be unforgiving.