David C. Weiss, the special counsel who spent years investigating Hunter Biden, issued his final report Monday on his work, criticizing President Biden for making “baseless accusations” that threaten “the integrity of the justice system as a whole.”

In a pointed rejoinder, Mr. Weiss wrote, “The president’s characterizations are incorrect based on the facts in this case, and on a more fundamental level, they are wrong.”

His inquiry had been a subject of fierce debate until the president issued a broad pardon that ended the case against his son.

The release comes amid a much more contentious 11th-hour legal fight over the publication of a report by Jack Smith, the special counsel who filed two indictments against Donald J. Trump only for both to collapse in part because of Mr. Trump’s 2024 election victory.

Mr. Weiss’s time as special counsel began after he had already investigated Hunter Biden for several years on tax, finance and foreign lobbying issues. The two sides briefly struck a plea deal, but the unusual nature of the agreement — in addition to the government’s unwillingness to promise that the investigation would end with the deal — resulted in its collapse in July 2023.

The failed plea led Mr. Weiss to seek and receive an appointment as special counsel, allowing him to file indictments against the president’s son in two jurisdictions — related to lying on a gun purchase form in Delaware, and tax charges in Los Angeles.

Last year, the younger Mr. Biden was convicted of the gun charge by a jury in Wilmington, Del. He pleaded guilty in the tax case, but his father pardoned him while he was awaiting sentencing in both cases. The president not only absolved his son of the convictions, but also gave him a sweeping pardon for any potential crimes covering a period of more than 10 years.

In doing so, the president said his son’s case had been infected with politics, a claim sharply disputed by Mr. Weiss and the Justice Department.

Mr. Weiss also indicted and won a guilty plea from another man, Alexander Smirnov, for lying to the F.B.I. during the 2020 election period by falsely claiming knowledge of corrupt payments to the father and son. Mr. Smirnov, a longtime F.B.I. informant, had claimed that executives from the Ukrainian energy company Burisma had paid Joseph R. Biden Jr. and Hunter Biden $5 million each around 2015 — an accusation that was trumpeted by congressional Republicans.