Considering that the Justic Dept has dropped cases against friends of the president (one of whom confessed to the crime of lying to the FBI to cover up for the president) and given that we're a couple months from an election where race is an issue, I also share your doubt about the Justice Dept being agnostic here.
You are making things up. Flynn was setup, his 302s were altered, FBI didn’t believe he lied, Brady evidence was not provided to his counsel (and still hasn’t been), he was bankrupted with over 6 million in legal fees, he had to sell both his houses, his old lawyers had severe conflict of interest which were not disclosed and he was threatened that they would go after his son if he didn’t plead guilty to something he never said. He was the incoming national security advisor - media makes it seem like the national security advisor talking to foreign countries after election is somehow an illegal thing? Now his judge has gone on a full circus.
Please research from non biased non spin news and look at actual documents unsealed.
There's also a perfectly reasonable argument on the facts to drop the case against Flynn - not least of all what appears to be motivated entrapment and no appropriate cause to investigate in the first place - but this becomes a politically charged argument and I feel it's inappropriate on HN.