If the judge agrees, the 67-year-old Stone will receive the harshest sentence of the half-dozen Trump associates convicted of crimes that include tax fraud and lying to investigators.
After Trump tweeted that the recommended sentence was a "miscarriage of justice," the Justice Department ordered prosecutors to abandon their position on sentencing.
At that point, the four prosecutors who won the Stone conviction, two of whom had previously worked on special counsel Robert S. Mueller III's probe of Russian interference in the 2016 presidential campaign, abruptly withdrew from the case. One resigned from the department.
Another prosecutor was tapped to take over. John Crabb, the chief of the criminal section in the U.S. attorney's office in Washington, wrote in court papers Tuesday that the original filing "does not accurately reflect the Department's position" and the prison recommendation was too severe.
Incarceration was warranted, Crabb wrote, but prosecutors deferred to Jackson to decide the appropriate sentence.
Both sentencing filings were approved by Timothy Shea, the acting U.S. attorney, court papers show. Shea was appointed Jan. 30, taking over for Jessie Liu, who had left the position pending her nomination to a senior Treasury Department position.
Trump on Tuesday withdrew Liu's nomination. An associate of Liu's said she believes Barr blamed her for the Stone debacle and "threw her under the bus with Trump."
"The president's allies think she is part of the 'deep state,' so it was easy to pin this on her," said the associate, who spoke on condition of anonymity to protect private conversations.
Former and current prosecutors were befuddled by the department's handling of the matter. They said Shea, a close adviser to Barr, was put in the job to help the attorney general supervise politically sensitive investigations.
Shea felt the recommendation was too harsh. So did Deputy Attorney General Jeffrey Rosen and his staff, former and current prosecutors said.