I've never actually gotten a straight answer from the right-wing about the motivations of the Deep State, or even what exactly constitutes the Deep State. There's only two things I'm sure of from what they say: 1) the Deep State is anti-Trump, and 2) it involves the intelligence agencies.

Trump says that the DOJ has been weaponized against him, eventhough many of the cases against him are at state levels. So what does the DOJ do about war crimes?

In speeches and news conferences, including on a surprise visit to Ukraine in June 2022, Garland condemned Russia's military onslaught and the "war crimes that the entire world has seen." The attorney general has repeatedly pledged that the Justice Department would do all it could to hold the perpetrators accountable.

It wasn't just talk. Garland also quickly established a special team to focus on possible Russian atrocities, an effort that led to charges late last year against four Russian soldiers for alleged war crimes in Ukraine. The U.S. is also assisting Ukrainian authorities with their own investigations.
...
It's unclear, however, whether the department's political will extends to the other major war raging right now — the one between Israel and Hamas.

Nearly six months into that conflict, Garland has said just 29 words in public about possible war crimes. Those remarks came at a news conference in December announcing the case against the Russians when he was asked by a Fox News reporter, "where are you on war crimes relating to Hamas?"

Garland replied: "Hamas murdered more than 30 Americans and kidnapped more during their terrorist attack on Oct. 7. We are investigating those heinous crimes, and we will hold those people accountable."

Garland made no mention of examining Israel's actions in the conflict.

In other words, the DOJ is doing EXACTLY what their bosses want them to do. Which is what you would expect from career bureaucrats.
Personally I think that is scary, considering the uninterrupted streak of one horrible president after another. However, this isn't the sort of independent scary that the right-wing says they are. I personally wish that the Deep State WAS more independent.
Then there is this example.

U.S. intelligence skews its findings to find favor with both Republican and Democratic policymakers, including former presidents Donald Trump and Barack Obama, a sweeping new study by the Pentagon-backed RAND Corporation finds. The study draws on interviews, some anonymous, with nearly a dozen current and former U.S. intelligence officials and policymakers.

Despite the popular “deep state” characterization of the intelligence community as a rogue army running roughshod over elected leaders, the study concludes the exact opposite. It portrays an intelligence community that naturally tilts its reports and forecasts to curry favor with presidents and their high-level policymakers in Washington, regardless of party or issue.

“Policymakers most frequently introduce bias in intelligence assessments from a desire to minimize the appearance of dissent, while the IC” — intelligence community — “tends to introduce bias through self-censorship,” the report says.

You mean they are acting like careerists and doing the bidding of their bosses, both Democrats and Republicans. I find this inexcusable and horrifying, but for the exact opposite reasons that the right-wing tells us.