I was on the depo-provera shot i stopped taken it about 3 months ago i am two months late on my periodand now i'm having brown discharge what could that mean?

A number of things: It can take 6 months after stopping a Depo-Provera shot before periods return to "normal" assuming they were 'normal' to begin with. You could have skipped a cycle, in theory you could have had an early pregnancy and early misscarriage. Many early miscarriages are perceived by women as a late or funny period. But you could have just had a funny period this cycle as well. Be healthy, wait and watch.