The 53-year-old son of the sitting president had appeared in federal court in July with the intention of pleading guilty to misdemeanor criminal tax charges.
His attorneys had reached a separate pretrial diversion agreement with prosecutors on an unrelated firearms charge.
But the plan fell apart after the presiding judge probed the prosecutor and Biden's attorney about the details of the agreement.
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Instead of putting his legal troubles in the rear-view mirror, Hunter Biden ended up pleading not guilty in that hearing on the charges of failing to pay federal taxes on more than $1.5 million annually in 2017 and 2018. That tax bill has since been repaid.
U.S. Attorney David Weiss and Biden's lawyers have since argued in dueling court filings over whether their prior agreement to let Hunter escape prosecution on the felony weapons charge is in effect.
"We believe the signed and filed diversion agreement [on the gun charge] remains valid and prevents any additional charges from being filed against Mr. Biden," Lowell said this month. The attorney emphasized that Biden "has been abiding by the conditions of release under that agreement for the last several weeks, including regular visits by the probation office."
Earlier in September, Weiss, who had been appointed special counsel in Hunter Biden's case by Attorney General Merrick Garland, signaled that prosecutors would file an indictment by the end of the month.
The indictment compounds the pressure the Bidens were already facing this week: On Tuesday, House Speaker Kevin McCarthy, R-Calif., directed Republican leaders in his chamber to open an inquiry centered on allegations that Joe Biden profited from his son's foreign business dealings while holding office.
White House officials have denounced the move, saying there is no evidence of wrongdoing by the president and slamming McCarthy for beginning the inquiry without holding a vote in the House, as he had previously vowed to do.
The indictment was made public just over an hour before the president, who is running for reelection in 2024, was set to deliver a speech in Maryland touting his economic agenda.
Weiss was appointed by former President , who is grappling with his own staggering criminal caseload as he campaigns for the 2024 Republican presidential nomination.
In reaction to news of Hunter Biden's indictment, Trump, who has claimed that the president's son is receiving special treatment, appeared to distance himself from Weiss.
"Prosecutor Weiss is appointed by the 2 Democrat Senators of Delaware under Blue Slip!" Trump on Truth Social.
In a follow-up post, Trump complained that the gun charge "is the only crime that Hunter Biden committed that does not implicate Crooked Joe Biden."
This is breaking news. Please check back for updates.
— CNBC's Brian Schwartz contributed to this report.
