What Causes Missed Periods?

I have the Mirena for my birth control for just under 2 years now. Shortly after I had it implanted my periods stopped, My boyfriend and i just had to be put on medication for Chlamydia and have been completely faithful to each other for the last 3 years. I also take showers every day and we followed the no sex rule during treatment. I'm showing symptoms again after two test came back negative and I'm wondering, since chlamydia is a bacterial infection, could not having a period cause it to keep coming back?