When it became clear that Ms. Liu would not stay until she was confirmed, it raised suspicions among some in the U.S. attorney’s office. Those were only compounded in late January when Mr. Barr designated Timothy Shea, a longtime trusted adviser, as her temporary successor rather than letting her top assistant serve as caretaker.
Mr. Shea arrived on Feb. 3 with David Metcalf, another perceived Barr loyalist, to serve essentially as his chief of staff. Mr. Metcalf immediately caused discord when he moved a prosecutor from her office so that he could work adjacent to Mr. Shea, according to two people familiar with the move. A Justice Department official said Wednesday that the office next to Mr. Shea’s had already been vacated.
One week later, they faced a dilemma when the four career prosecutors working on the Stone case proposed recommending a sentence of seven to nine years, in line with nonbinding federal sentencing guidelines.
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On Monday, several people familiar with the matter said, Mr. Shea told the prosecutors that he wanted a lower sentence, reminding them that they had discretion to deviate from the guidelines. But three of the four prosecutors threatened to quit the case, so Mr. Shea acquiesced until Mr. Barr and the deputy attorney general, Jeffrey A. Rosen, overruled him on Tuesday.
It was unclear how much Mr. Shea told his superiors about the final recommendation before it was filed, but department officials maintained they were not given adequate information.
At the same time, Mr. Trump withdrew Ms. Liu’s nomination for the Treasury post. Mr. Mnuchin told a Senate committee on Wednesday that he learned about the decision on Monday but declined to elaborate.
Morale sank inside the Washington office after the intervention on the Stone sentencing, and some prosecutors expressed skepticism that senior Justice Department officials were not adequately warned about the recommendation.
On Wednesday night, Mr. Shea told staff members that he respected their work and vowed to “do my best” to support it, according to an email he wrote to the office that was reviewed by The New York Times.