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Hunter Biden's plea deal fell apart during his first court appearance Wednesday morning and he pleaded "not guilty" as federal prosecutors confirmed the president's son is still under federal investigation. 

Hunter Biden was expected to plead guilty to two misdemeanor tax counts of willful failure to pay federal income tax, as part of plea deal to avoid jail time on a felony gun charge.

HUNTER BIDEN AGREES TO PLEAD GUILTY TO FEDERAL TAX CHARGES

Hunter Biden leaves court

Hunter Biden, son of President Joe Biden, departs the J. Caleb Boggs Federal Building on July 26, 2023 in Wilmington, Delaware. Biden pleaded not guilty to two misdemeanor tax charges in a deal with prosecutors to avoid prosecution on an additional gun charge. However, the federal judge overseeing the case unexpectedly delayed Biden’s plea deal and deferred her decision until more information is put forth by both the prosecution and the defense. (Anna Moneymaker/Getty Images)

But Judge Maryellen Noreika did not accept the plea agreement, questioning the constitutionality — specifically the diversion clause and the immunity Hunter Biden would receive.

Hunter Biden was also expected to enter into a pretrial diversion agreement regarding a separate felony charge of possession of a firearm by a person who is an unlawful user of or addicted to a controlled substance.

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The judge pressed federal prosecutors on the investigation and questioned whether there was the possibility for future charges, and asked prosecutors if Hunter Biden was currently under active investigation. Prosecutors said he was, but would not answer specifically what the president's son is under investigation for.  

Prosecutors on Wednesday, though, said Hunter Biden pleading guilty to the two misdemeanor tax offenses would not immunize him from future charges. 

Hunter Biden in Delaware court

A courtroom sketch depicting Hunter Biden in a federal courtroom in Wilmington, Delaware on July 26, 2023. (COURTESY: William J. Hennessy, Jr.)

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At one point, Noreika asked Justice Department prosecutor Leo Wise whether there is an "ongoing investigation here." 

"There is," Wise said, adding that he could not tell the judge what the investigation was. 

Noreika asked if the government could potentially bring a charge related to the Foreign Agents Registration Act (FARA), to which Wise replied: "Yes." 

At that point, the original plea deal broke down. Defense attorney Chris Clark said he did not agree with that. 

"Then there’s no deal," Wise said. 

Clark countered, "As far as I’m concerned, the plea deal is null and void."

Hunter Biden’s legal team exits court

Hunter Biden’s legal team exits a Federal Courthouse at the Caleb Boggs Federal Building in Wilmington, Delaware on Wednesday, July 26, 2023. The president’s son plead not guilty to two misdemeanor charges after his  plea deal was rejected. (The Image Direct for Fox News Digital )

After that, both sides asked the judge for time to negotiate. Noreika left the courtroom for 20 minutes or so and allowed both sides to continue negotiations. 

Ultimately, Hunter Biden pleaded not guilty because Noreika could not accept the plea deal as it was constructed. She repeatedly expressed her concerns about the constitutionality of the diversion deal related to the felony gun charge, specifying that the main issue with the agreement was that if Hunter Biden breached the deal, the judge would need to make a finding of fact on the matter before the government could bring charges. 

Judge Noreika said she saw that as being "outside of my lane," noting that if the diversion agreement might be unconstitutional, then the entire plea deal would be unconstitutional, meaning that Hunter Biden would not be getting the immunity he thought. 

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The diversion was an agreement in which the government would not charge Hunter Biden with the more serious federal gun charge — if he pleaded guilty to the misdemeanor tax charges and behaved under certain terms of the agreement for a period of approximately 24 months. If Hunter Biden breached the diversion, the government would try to bring the serious gun charge against him.

At that point, the government would bring that information to the judge, and the judge would be required to determine whether charges should be brought — that was the portion of the diversion which Noreika rejected, saying that would be unconstitutional, as charging decisions are made by the executive branch, not the judicial branch.

Hunter Biden’s legal team exits court

Hunter Biden’s legal team exits a Federal Courthouse at the Caleb Boggs Federal Building in Wilmington, Delaware on Wednesday, July 26, 2023. The president’s son plead not guilty to two misdemeanor charges after his  plea deal was rejected. (The Image Direct for Fox News Digital )

Meanwhile, the judge apologized to Hunter Biden near the end of the hearing. 

"Mr. Biden, I know you want to get this over with, and I’m sorry," Noreika said. "But I need to get more information to do justice as I’m required to do."

The judge asked for briefings from both sides, but did not set a firm date. 

Noreika questioned Hunter Biden on his sobriety, and on his business dealings — specifically money that he received from foreign business partners, like Ukrainian natural gas firm Burisma Holdings and his joint-venture with Chinese energy firm CEFC. 

As Hunter Biden pleaded not guilty, White House press secretary Karine Jean-Pierre delivered a statement at the beginning of the daily briefing.

"Hunter Biden is a private citizen, and this was a personal matter for him. As we have said, the president, the first lady — they love their son and they support him as he continues to rebuild his life," Jean-Pierre said. "This case was handled independently, as all of you know, by the Justice Department under the leadership of a prosecutor appointed by the former president, President Trump." 

DOJ OFFERS HUNTER BIDEN INVESTIGATOR FOR TESTIMONY BEFORE THE HOUSE

Hunter Biden court sketch

A courtroom sketch depicting Hunter Biden in a federal courtroom in Wilmington, Delaware on July 26, 2023. (COURTESY: William J. Hennessy, Jr.)

She added: "So for anything further, as you know, and we've been very consistent from here, I'd refer you to the Department of Justice and to Hunter's representatives who is his legal team, obviously, who can address any of your questions." 

The developments in the case Wednesday come after IRS whistleblower testimony revealed allegations of DOJ misconduct throughout the yearslong investigation into the president's son. IRS whistelblowers Gary Shapley and Joseph Ziegler said politics influenced prosecutorial decisions throughout the investigation. 

House Ways & Means Committee Chairman Jason Smith filed an amicus brief to the court, requesting that testimony be considered ahead of accepting the planned plea deal, saying Hunter Biden "appears to have benefited from political interference which calls into question the propriety of the investigation of the U.S. Attorney’s Office." 

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Hunter Biden arrives to court in Delaware dressed in a suit

Hunter Biden arrives to a Federal Courthouse at the Caleb Boggs Federal Building with his lawyer, Kevin Morris in Wilmington, Delaware, Wednesday, July 26, 2023. President Joe Biden's son is reportedly expected to plead guilty during the hearing to two federal crimes for not paying taxes on time. (The Image Direct for Fox News Digital)

"In the interest of full transparency and fairness for all citizens, it is critical for the Court to have this relevant information when evaluating the Plea Agreement," Smith wrote in the brief. 

Meanwhile, on the eve of the court appearance, the judge threatened to sanction Hunter Biden's legal team after one of his attorneys allegedly lied about who she was while asking to remove IRS whistleblower testimony from the court docket. 

The defense, though, denied the allegations and called the incident "an unfortunate and unintentional miscommunication." 

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Fox News' Griff Jenkins and Alexandra Rego contributed to this report.