JAG, the series, is a pro-military series and when it points out issue with the U.S. Navy people stop to listen.
Mishap is just such a time. Harm's defense (suggested by a former squadron partner) was to point out the issues with operational readiness. Harm forces the issue, obtains the documents, and we hear about issues in the U.S. Navy. The writers and producers give us the large picture by seeing the role Congress and even President has in making and solving these issues.
Yet in the end, JAG (the writers, producers, and Harm) remembers the old saying Henry Ford once said, "Navy is never wrong, but in this case it was a little weak on being right."
In the end Harm asks the members to view the defendant in the same light as they view all the others who had a hand in conditions on board the ship before and during the mishap.
Yes Johnny, sometimes you can have your cake and eat it, too.
Oh, and we see where Harm was able to pull off a defense Mac couldn’t. Now maybe we have an indication who is the better lawyer.