If you don't have condoms you need to be abstaining from sex. Pulling out offers you no protection at all, and leaves you very much at risk of pregnancy. You both need to be more responsible about sex if you think you're mature enough to deal with the consequences of it. Go back to the doctor and request a beta blood test. You need to find out what your hCG levels are at -- if they are under 5, you are not pregnant.
Aside from the obvious that you should be on some type of birth control, and knowing that condoms or pulling out are never 100% effective - if you had a negative test at a doctors office, you are more than likely not pregnant. Stress can delay your cycle, as well as changes in diet, changes in physical activity, and change in age. At 15, your body is not fully developed and will be constantly undergoing changes for the next few years. I won't lecture you on having sex at 15 because you are already doing it. Birth control, even a low dosage, combined with condoms can greatly reduce your chances of getting pregnant. Birth control can also help regulate your cycle, clear skin (if that's an issue), and help control out of whack hormones that may be causing your cycle to change. If you are afraid to talk to your parent or guardian, you can go to a free clinic that will offer birth control until you are 18.