Amid a growing storm Tuesday within the Justice Department over its unorthodox intervention in the sentencing recommendation for Roger Stone, a longtime ally of President Trump, officials maintained that there was nothing untoward about what happened. They said the decision was made independent of Trump’s very public gripes about the matter. They said it was the result of a “breakdown” in communication.

Then Trump tweeted.

The president took to Twitter on Wednesday morning to congratulate Attorney General William P. Barr for “taking charge of a case that was totally out of control and perhaps should not have even been brought.”

The president’s implication: This was his own, appointed attorney general — whose repeated interventions in Trump’s favor have caused almost constant controversy — getting involved to lighten the sentencing recommendation for Trump’s own ally.

The tweet may not directly contradict the Justice Department’s version of events Tuesday, but it sure colors it in a different way. In one tweet, Trump appeared to confirm reports that Barr has taken an interest in matters that involve the president personally. And there are growing questions about whether that’s just on the Stone matter.

Roger Stone was sentenced to 40 months in prison on Feb. 20, after being convicted of lying to Congress, witness tampering and obstruction of justice. (Adriana Usero/The Washington Post)

The Justice Department also recently scaled back its language in recommending a sentence for former Trump national security adviser Michael Flynn. It was initially zero to six months, and in that early January filing, prosecutors referred to Flynn’s offense in stark terms. But later that month, a filing added that probation was a “reasonable” sentence and more effusively referred to Flynn’s long service in government. It was a pretty noted change in tone that turned heads at the time. And it came despite Flynn now attempting to withdraw his guilty plea for lying to investigators.

That shift takes on new significance with Trump’s Wednesday tweet. It’s difficult not to read it as him linking Barr directly to these kinds of decisions, whether that’s actually the case.

The latest intervention has triggered a mass protest from the prosecutors who handled the Stone case. All four withdrew from the case, and two of them resigned positions in the Justice Department. The exodus appeared to confirm that there was dissension among the prosecutors over more senior Justice Department officials intervening to call for a lesser sentence. Former Justice Department officials cried foul over alleged political influence in what is supposed to be an independent prosecution.

The initial recommended sentence of seven to nine years was harsh, but it was within the guidelines for the seven counts on which Stone was convicted — a situation in which prosecutors are generally given discretion to make a recommendation. An anonymous senior Justice Department official said Tuesday that the recommendation was considered “extreme and excessive” and that the prosecutors hadn’t accurately communicated what it would be up the chain of command.

Even if that’s what happened, this was still senior Justice Department officials intervening in an unusual way — and in a case of distinct personal interest to the president. Even if Trump hadn’t directly lobbied for the decision, it would be problematic, because it suggests that his political appointees are riding to the aid of his allies, over the judgments of prosecutors handling the cases. A Justice Department official on Tuesday couldn’t name another instance in which a sentencing recommendation had been overturned so quickly. And now Trump is linking this personally to Barr — the man whose conduct on the Russia investigation has erred repeatedly in Trump’s favor.

Trump has essentially argued that there is nothing wrong with such an intervention, even if he had directly ordered Barr to take such actions (which Trump denies having done in this case). Speaking to reporters Tuesday, Trump said that he “would be able to do it if I wanted” and that “I have the absolute right to do it.” Trump routinely claims such broad authority, but generally the Justice Department guards against perceptions of political influence in investigations — and that’s particularly important in cases involving the president and his allies.

We’ll surely learn more about how all that went down in the days to come. But Trump’s tweet sure didn’t diminish the idea that his Justice Department is doing his political bidding — starting at the top.