Are you a midshipman or not? Because if so, your NROTC/USNA CoC should be advising you how to proceed.
If not, I don't have any insider information as to how NR screens applicants, but if you were denied a GPA waiver then I would start pursuing other career options. Try to raise your GPA next year and reapply (if you're allowed to). Other Naval communities care more about the 'whole person concept' than nuke, which is why you never did interviews or submitted statements. Also, other designators care about your ASTB score a lot more, which can help offset a low GPA. But these days business is good for officer applicants so cross your fingers but don't hold your breath.
Also, it's good that you decided to be a hard-charger and load up on tough coursework, but didn't any school advisor ever tell you that no one gives a crap about excuses for sub-par performance? With HR processes becoming more automated, it becomes a numbers game and if the GPA doesn't pass the filter, no one's going to scrutinize your credentials any further. Not every company is like that of course (such as other Navy officer communities), but you didn't do yourself any favors by taking coursework that you couldn't handle.