Attorney General Bill Barr and his allies are centralizing control over the Justice Department and acting in increasingly blatant ways to protect President Donald Trump’s interests and allies.

This became evident in dramatic fashion Tuesday when the entire team prosecuting longtime Trump adviser Roger Stone withdrew from that case after Justice Department higher-ups made clear they planned to override their sentencing recommendation.

But the Stone controversy was just the latest in a series of recent moves by Barr to “take control of legal matters of personal interest to President Donald Trump,” as Carol Lee, Ken Dilanian, and Peter Alexander of NBC News reported.

Senior Justice Department officials also intervened to change the sentencing recommendation for another Trump ally, Michael Flynn, last month. Barr put in a close ally in the politically sensitive US Attorney’s Office for the District of Columbia job (in a procedurally unusual way). And Barr instituted new rules requiring his personal approval for any new investigations into presidential campaigns, staff, or foreign contributions — something that naturally would help the investigation-plagued Trump campaign.

All this has unfolded as Trump has separately taken revenge on witnesses in the impeachment inquiry: dismissing Alex and Yevgeny Vindman from the National Security Council staff and firing EU Ambassador Gordon Sondland. The president also pulled a Treasury Department nomination for the former US Attorney for DC, who had supervised Stone’s prosecution.

It’s not clear whether Barr is acting in response to explicit private instructions from Trump, but it’s largely irrelevant. Trump has made it unmistakably clear that these are the sorts of things he wants Barr to do — he tweeted before the change to Stone’s sentencing recommendation that it should be changed, and he praised Barr personally for doing so afterward.

This is a horrible and very unfair situation. The real crimes were on the other side, as nothing happens to them. Cannot allow this miscarriage of justice! https://t.co/rHPfYX6Vbv — Donald J. Trump (@realDonaldTrump) February 11, 2020

Congratulations to Attorney General Bill Barr for taking charge of a case that was totally out of control and perhaps should not have even been brought. Evidence now clearly shows that the Mueller Scam was improperly brought & tainted. Even Bob Mueller lied to Congress! — Donald J. Trump (@realDonaldTrump) February 12, 2020

It’s a grim situation at the Justice Department. In cases involving President Trump and his allies, it seems career prosecutors will no longer have their judgment respected; instead, Barr will be waiting in the wings to overrule them if he deems it necessary.

Barr’s moves center on the US Attorney’s Office for the District of Columbia

The full story of what’s going on behind the scenes at the Justice Department remains murky, but many of the recent eyebrow-raising events have centered on the US Attorney’s Office for the District of Columbia.

Many of the most important federal prosecutions involving top US government officials end up getting brought by the US Attorney for DC — because, well, that’s where the government is.

Since September 2017, that post had been filled by Jessie Liu, a veteran of the George W. Bush Justice Department who wasn’t particularly viewed as a “Trump person.” Liu’s office took over Roger Stone’s prosecution once special counsel Robert Mueller’s team wrapped up and pursued it vigorously, winning his conviction at trial. Her office also took over the sentencing process for Michael Flynn and Rick Gates, both of whom were charged in Mueller’s probe. There was no indication she was going easy on Trump allies.

Additionally, Liu’s office handled two other controversial cases that seem to have ended in embarrassing ways for the administration. Her prosecutors indicted former Obama White House counsel Greg Craig for false statements related to his work with Paul Manafort, but Craig was acquitted at trial. Her team also investigated former Deputy FBI Director Andrew McCabe, a frequent Trump target, for alleged false statements related to a leak — but though leaks suggested McCabe would be indicted, no indictment materialized, for unclear reasons.

In December, President Trump announced his intention to nominate Liu to fill a Treasury Department post. This seemed to be an ordinary enough personnel change after Liu had spent over two years in the post — though she had to be confirmed by the Senate first.

Then, on January 7, the trouble began.

Michael Flynn’s sentencing appears to have been the first problem

It started with a new sentencing memo Liu’s office filed regarding Flynn, Trump’s former national security adviser who pleaded guilty for lying to the FBI about his contacts with the Russian ambassador.

Flynn had initially pleaded guilty to this charge in December 2017 and agreed to cooperate with Mueller’s team. Things seemed to be going according to plan as his December 2018 sentencing hearing approached; prosecutors wrote that a sentence that “does not impose a term of incarceration” would be appropriate for him.

Surprisingly, though, at that hearing, the judge in Flynn’s case, Emmet Sullivan, raked Flynn over the coals, saying he felt “disgust” and “disdain” for what Flynn did, and strongly suggested he might give Flynn some prison time. However, Sullivan offered Flynn the opportunity to delay his sentencing to get credit for further cooperation with the government, and Flynn jumped at the chance.

Yet instead of cooperating further, Flynn decided to dump his lawyers and hire a conservative firebrand, Sidney Powell. He also did not agree to give prosecutors the testimony they wanted in a case against one of his business associates, Bijan Rafiekian. Filings from Powell grew increasingly defiant, seeming to reject Flynn’s previous acceptance of responsibility for his false statements and imply that Flynn had been set up by the government. (Powell eventually filed a motion to have Flynn’s guilty plea withdrawn.)

The prosecutors in Flynn’s case were not at all happy with this turnabout, and as his new sentencing date approached, they let Judge Sullivan know in a January 7 filing.

“Given the serious nature of the defendant’s offense, his apparent failure to accept responsibility, his failure to complete his cooperation” in Rafiekian’s prosecution, “and the need to promote respect for the law and adequately deter such criminal conduct, the government recommends that the court sentence the defendant within the applicable Guidelines range of 0 to 6 months of incarceration,” prosecutors wrote.

That is: They had changed their recommendation, and now think Flynn may well deserve to be locked up. And Liu signed off.

Yet about three weeks later, as filings back and forth from the prosecution and defense continued, the government curiously shifted its position. Now, prosecutors stressed, they agreed with the defendant “that a sentence of probation is a reasonable sentence.”

According to NBC News, this change came about because “senior officials at the Justice Department” intervened. Liu, again, signed off.

That same day, she exited her job.

Liu was replaced — before she had been confirmed to her new post — with a Barr ally

Liu’s exit from the US Attorney’s job was odd. Yes, she had been nominated for something else in the Treasury Department, but she hadn’t yet been confirmed for it by the Senate. And her confirmation hearing was expected to take place in just a few weeks, so it was unclear why there needed to be such haste in removing her.

Indeed, the New York Times reports that Liu “initially told colleagues that she would stay on as U.S. attorney until the Senate confirmed her” — but that she and Barr “then agreed that she would leave early in the new year so that someone else could run the office if the confirmation process stretched on.”

And the identity of Liu’s replacement may help clarify things. The interim US Attorney for the District of Columbia would be Timothy Shea, one of Barr’s “closest advisers” (per the Associated Press). Shea had been serving as a counselor to Barr at the Justice Department.

Shea’s appointment can certainly be interpreted as an attempt by Barr to bring this US Attorney’s office and all the politically charged cases it handles under his control — or, at the very least, under the control of a trusted ally.

And the timing of the Flynn sentencing dust-up certainly raises questions of whether Shea was slotted in — and Liu was pushed out — very quickly in an attempt to prevent something similar from happening again.

Then something similar happened with Roger Stone

By this Monday, it was time for another high-profile sentencing recommendation from the US Attorney’s Office for the District of Columbia. This one involved Roger Stone, the longtime Trump adviser who was convicted last November on seven total counts of obstruction, false statements, and witness tampering.

The probation office had calculated that guidelines for a sentence for Stone’s crimes would be between 87 and 108 months (about seven to nine years). And prosecutors told the judge in Stone’s case that such a sentence would indeed be “appropriate.” The new interim US Attorney, Shea, signed on.

Trump flipped his lid. “Cannot allow this miscarriage of justice!” he tweeted at 1:48 am on Tuesday.

And later in the morning, word leaked out to a Fox News reporter that indeed the Justice Department would not allow this recommended sentence.

Anonymous Justice Department officials have insisted to various reporters that they were not responding to Trump’s tweet in doing this, and that the decision to override the prosecutors was made before the tweet. This claim has been greeted with much skepticism.

As for why Shea allowed the sentencing recommendation in the first place, the New York Times reports that one official claims there was a “breakdown in management” and no clear approval was given by top officials.

Whatever happened, it’s extraordinarily unusual for federal prosecutors to walk back their sentencing recommendation the very next day. And once it became clear that’s what would happen, all four Stone prosecutors withdrew from the case in apparent protest. (One, Jonathan Kravis, quit the Justice Department entirely; the other three are remaining.)

After that, a new prosecutor on the case, John Crabb, submitted a filing to the court saying that the previous sentencing memo for Stone “does not accurately reflect the Department of Justice’s position on what would be a reasonable sentence in this matter.” Crabb wrote that the government believes “a sentence of incarceration far less than 87 to 108 months’ imprisonment would be reasonable under the circumstances” — but that they’ll defer to Judge Amy Berman Jackson on what exactly that would be.

The capper on this, for now, occurred Tuesday evening, when Axios’s Jonathan Swan reported that Trump would in fact withdraw Jessie Liu’s nomination to that Treasury post — a move that meant she would not testify before a Senate committee at a scheduled confirmation hearing later this week. Whether this is an effort to retaliate against the person who oversaw Stone’s prosecution or simply an attempt to avoid ugly testimony, it certainly makes Liu’s ahead-of-schedule replacement by Shea look even more questionable. (Liu resigned Wednesday night.)

Meanwhile, Barr ensured Trump can’t be investigated without his approval

That’s all the recent action (that we know of) from this single US Attorney’s office, but Barr has also made a much more wide-ranging change that could be of massive importance to President Trump.

NPR reported last Thursday that Barr has instituted a new Justice Department rule requiring his personal approval for the opening of any investigation of a presidential candidate, a campaign, campaign staff, or a potentially illegal foreign contribution.

Remember: Trump’s 2016 campaign was eventually plagued not just by the Russia counterintelligence investigation but also by an investigation into hush money for Stormy Daniels (Michael Cohen eventually pleaded guilty to violating campaign finance law with the payments). There have been various investigations of foreign money potentially making its way to the Trump campaign or allied groups (as well as some involving foreign money to Hillary Clinton’s campaign).

What Barr is ensuring with this new rule is that there will be no surprises from pesky independent-minded investigators. If it touches a presidential campaign, he will have to sign off on it.

How he will use that authority isn’t yet clear. But he and his allies at the top of the Justice Department have already shown a distinct willingness to intervene in procedurally unusual and inappropriate ways in cases of interest to President Trump.

So how bad are things?

Despite all the drama over the sentencing recommendations for Flynn and Stone, we should note that in both cases, the final decision on sentencing lies with a judge, not prosecutors. So, inappropriate though these moves may be, it’s not clear if they will actually change anything. (Trump does, of course, have the power to pardon both of them or commute their sentences.)

Beyond that, there are some complications to the narrative that the Justice Department is being entirely bent to serve President Trump’s interests.

For one, Rudy Giuliani’s close allies Lev Parnas and Igor Fruman were arrested last October and indicted by prosecutors from the US Attorney’s Office for the Southern District of New York (SDNY) for campaign finance violations.

Parnas, Fruman, and two other defendants are awaiting trial, and prosecutors have said they expect to file a superseding indictment at some point with further charges. This continuing probe reportedly imperiled Giuliani as well. One would think that a Justice Department wholly responsive to Trump’s whims would not be investigating his lawyer.

But though this investigation is headed by SDNY, an office with a reputation for independence, there have been reports that Justice Department leaders in Washington later got involved as well. The current state of the investigation remains unclear.

Other politically controversial choices also await. Barr has appointed John Durham, the US Attorney in Connecticut, to head a freewheeling investigation into purported malfeasance from Trump-Russia investigators. The Justice Department is deciding whether to charge Trump ally Erik Prince with lying to Congress and violating US export laws. The Andrew McCabe investigation is still hanging out there without a clear resolution. News even broke recently that prosecutors were investigating James Comey in connection with years-old leaks.

In all these cases, is the Justice Department going to act like President Trump’s political attack machine (or defense mechanism)? Or is it going to respect the judgment of its prosecutors and weigh cases carefully before bringing charges? We’ll have to wait and see. But the signs from Barr of late have not been encouraging.