It sounds as if there are several issues here.
One...the guilt you feel for violating God's commands.
Two...the fear of becoming a father far before you're ready.
Three...school stress.
Four...depression.
First and foremost, if you haven't already done so, repent of sexually sinning with your girlfriend and ask forgiveness. (Repent means...don't do it anymore!)
God will not hear our prayers if we are willfully sinning against Him. But, He will always, fully and graciously, forgive us our sins.
Two...as Chris said, a missed period may not necessarily mean she's pregnant...and even if she is pregnant, she may miscarry...many women do miscarry their first...then again many don't. You should have her take a home pregnancy test...inexpensive, simple to take and quite accurate. Once you find out for sure that she is pregnant...then you can start making concrete plans on what to do, should the baby not miscarry. Naturally, being the guy...your views on the subject can be completely overruled by your girlfriend, but, nonetheless, you can start discussing with her how to move forward. If the two of you are open to it, believe me, there are many couples out there who will be more than willing to adopt a baby.
As for the school stuff...yep, it's gets pretty rough. Work with your counselors to see how to manage it all.
And for the Depression...there are a lot of ways to handle depression non-pharmaceutically, and given your age, I'd suggest looking into them. Getting plenty of exercise, fresh air and sunshine can do wonders...even when you feel you have to drag yourself out of bed to do it.
Once you've repented and asked forgiveness of God (and to be sure, His forgiveness will be forthcoming) do remember that God doesn't take us out of bad situations, but He does help us through them.
Meanwhile, I'm glad that you're asking your Christian brothers and sisters to pray for you that God will help you through all this...(goes for your girlfriend as well!)