My Body is Acting all Bizerk!

Hello ladies! My first post and usually, I just sit back and educate myself from what you guys post. But I have a question and I need insight, please! 
I just recently retired from the military and I got on birth control (first the IUD) after I was sexually assaulted by my squad leader. Truthfully, the crap sucked and kept moving into my cervix so that was a no go! I went without birth control for a while; I had no reason to use it. && then, my boyfriend and I hooked up and I got on the depo shot. It made me feel weird at times, sometimes I wanted him ALLL the time and others I couldn't seem to get 💦. 👀👀 
I got out of the military and before I could get into the VA system, I had missed a shot. 3mo had gone by and I had a period. It hurt so badly that I wanted to get back on birth control just so it would stop! 😂 
Anyway, I've said all that to say: 
According to <a href="https://play.google.com/store/apps/details?id=com.glow.android.eve">Eve</a>, I was going on 45 days late (Bc I don't know exactly how to work this thing yet!) and just the day before my 25th, Aunt Flo decides to come.. Or does she? 
One day it's barely light red spots. The next it's dark brown blood. It's very inconsistent, but tomorrow (today in less than 40mins) will be a week. Is this a period? Why the bad blood?! Should I talk to my gyno? 
I haven't had sex since August, my man is heading back overseas so... Something's wrong!