Hi, and thanks for your query on eHealth forum!
Since you have been on depot shot of two years, chances of pregnancy are less. I suggest you wait for 14 days since spotting and go for blood HCG estimation as this is a more reliable test for pregnancy. If this is negative, then nausea, bloating etc are probably due to ovarian cysts which can cause abnormal glucose and hormone balance.
There are various approaches to treat a polycystic ovary. First of all insulin resistance has to be checked and corrected by a dose of metformin. You will also have to undergo complete hormonal profile including FSH, LH, estrogen, progesterone, prolactin, and thyroid hormones. Then regular check ups have to be scheduled and you put on low dose birth control pills to regularize the cycles first. Once this is corrected, regular ultrasounds will be done to assess the status of the ovum and accordingly drugs prescribed. At times laparoscopy is done and cysts punctured. Diet and weight control are also important part of therapy and you need to be under a good nutrition expert.
Since a confirmed diagnosis cannot be given on net please consult your gynecologist to find the cause. Hope this helps. Take care!