I had my first Depo shot in March. I suffered really irregular periods from this and decided I wasn't going to return for my second shot. All sign of bleeding seemed to begin to stop completely in the 10th week, although at this time I wasn't even having sex anyway.
Recently I have had unprotected sex in the 13th week of the shot "running out". I've heard you are protected up UNTIL the 13th week. I had sex 2 days after the specified time. This was now effectively 4 days ago. Since then I have been experiencing random cramping in my stomach, neck aches, and brown discharge (which only began this morning). I am just wondering what the chances are that I could be pregnant? Or could these just be side effects of coming off the Depo injection? I've heard it can take a long while for a woman's fertility and ovulation to get back to normal after the injection, so surely if I have gotten pregnant TWO days after the recommended time, would be highly unlucky right?
Obviously it is too soon to take a pregnancy test yet, as it is only 4 days after intercourse. But I am worrying that this "brown discharge" could in fact be implantation bleeding? Or am I just kidding myself and reading too much into this?

You're probably reading too much into this, but that is a probably which means there's a maybe not. What you stated about your fertility after the depo shot is true. What you stated about the end of the shot is also true. The "protection" up to the 13th week generally means that you're at the highest probability of not conceiving up to this point, which is when the rollercoaster started and you started experiencing what you're experiencing. This is your body getting back on track and getting things in order. The brown discharge sounds like old blood and just random break through bleeding not implantation bleeding. Implantation bleeding is like most things people research on the internet, if it's rare than EVERYONE believes they have it and especially if it is rare.

As I said before, your body is getting back on track managing its own fertility cycle. This means that you could get pregnant quickly, or it could take a while. If you're not ready to have a child than you should use another form of birth control at this point. I would recommend this if you're still playing power games in your relationship. This is in reference to the thread your started three months back in the Adult Sexuality board.

While possible, it would be unlikely that you became pregnant. You would still be considered covered by your first injection. It would be too early for noticing possible implantation bleeding.

As was said, be sure to use another form of birth control to lessen the chance of an unplanned pregnancy.