What exactly is going wrong in my fitness?

Ok, ever since i was very little up about 10th grade, i had a very flabby body. i had a beer belly and had a lot of flabby fat. However, mysteriously around the summer going into 11th grade, i lost most of my flabby fat except for my stomach. So im in 12th grade right now and i've been going to the gym for about 3 months. Problem is, i haven't gained almost any muscle and i still have a large amount of flabby fat around my stomach. in other words, im skinny, but i "look fat" around my torso. So what exactly do i need to do so i can gain muscle and also lose the flabby fat i have there? I use no protein at all, but now that i have seen no results, i plan to use an average amount.