HARBOR

It never hurts to apply. The worst case scenario is they say no and you put a stronger package together next time. I guess I'm confused what you're asking. If you're trying to decide between not applying for fear of rejection or applying with your current package, I'd say apply. Most school sincerely do look at the "whole person" concept. Are you applying for a masters degree or PhD? Try to focus on strengthening your application where able: strong statements, good LoRs, etc.

I would imagine it's more likely to move from an MA in a related field to a PhD. What would your PhD be in? I know several people with underwhelming undergraduate histories who have gone that route with mixed success. The biggest detriment to pursuing an MA outside of a PhD is the cost. But, because it sounds like you're going to utilize military money, that shouldn't be a problem. With regard to your question about admissions, having independent funding is definitely not going to hurt you. My focus would be to make sure that there is somewhat of a linear trajectory from MA to PhD (ie: MA in international relations to political science PhD). When I think "professional-oriented" masters in this field, I tend to think MPA/MPP, which are not necessarily a great transfer to a political science PhD.