Two things I’ve read that may prove to be relevant:
1. Flynn’s plea may have at least in part involved dropping an investigation of his son, who most likely had little to do with the Trump campaign but more to do with other dealings:
https://www.nbcnews.com/news/us-news/mike-flynn-s-son-subject-federal-russia-probe-n800741
2. Some say Flynn has had a bellyful of Obama for a long time and has a LOT that he wants to say about things. An honorable man would not hesitate to make a personal sacrifice (i.e. plead to this process charge) in order to have credibility to share other information.
Lastly - remember “fog of war” and the high probability that everything we think we “know” now will not all prove to be true in the final analysis. Take a breath, there’s nothing anyone here can do about any of this, just let it unfold and examine the outcome after things have cooled down.
And let’s just think about why this all started: a wiretap and unmasking of General Flynn...and who might be culpable for those acts.
Flynn himself is major spook ... looks very composed at Court. He was fired by Obama and knows where bodies are.