If you have any tendency to gain weight...DO NOT take this shot. I took two of those shots, cried for 6 months and gained 50 lbs. It was an aweful experience. I am very sensitive to hormones...I can't even take the pill without wanting to quit my job, leave my husband, etc. The bad thing about depo is that you can't just yank yourself off of it. You have to wait the few months for it to wear off.
Having said all of that, I have known a few people who have taken depo with no side effects, but they were very naturally thin people. Perhaps you are, too.
Coincidentally, I have ovarian cysts. Ask your doctor about taking Glucophage (generic is Metformin) for cyst reduction. That is what I am on right now.
If you are not seeing an OB/GYN for your cysts, I highly suggest switching to one for a second opinion on treatment.
I hope it all works out for you,
A.