If you find out through a CT that your pain is not caused from a kidney stone, what might be the other causes of the pain?

If you had a CT scan... you've been to a doctor... more than once. You should have had this discussion with them. There are a vast number of things that can cause pain... they have access to your medical records and history that can narrow that list substantially.

I don't see how you can declare your pain to be in your kidney. And a CT scan would show many conditions other than stones.
Just for starters, pain is often referred from other areas, so pointing to where your kidney is doesn't prove anything.
We don't know your history, age, gender, general health, or even which side you are talking about!

If you mentioned kidney, then you have had other issues with this in the past. If you are a diabetic with previous kidney problems, then it is an urgent situation. You have to be proactive regarding your health, discuss any symptoms with your doctor. Could be your life depends on it, so I don't know why people hesitate to tell all to their doctor.

If it is not kidney stones and your doctor previously had mentioned it may have something to do with your kidneys, then you can't LIVE without kidney function.

Although your saying its pain in the kidney area, the culprit can originate from almost anywhere. i.e. heart attack can radiate down your left arm, but it can also be found with shoulder pain in the right extremity. If you have a wallet in your back pocket, it can put pressure on the psyatic nerve, (back and leg pain).
Assuming the Dr examined your kidneys for CA. and told you to go home, either he is a bad DR. or you really have to look at your own activities in your life, that may be contributing factors. Bed, sports, etc. good luck