This is a tricky situation, you've missed your period and are having stomach pain, I think that warrants a trip to a clinic. Sorry I couldn't be more assistance I wish you luck.
There are many reasons why you could be experiencing this- PCOS, endometriosis, cyst, etc. Many things can play into what is going on- exercise, obesity, underweight, stress, etc. It is important to see a doctor to see what's going on.