Why does my knee crack and heart?

My knees make cracking sounds when i squat or do similar exercises and after that i have knee pain, the pain is like hundreds of needles are cutting my knee from inside and plus to all that my medial collateral ligament hearts but only when i walk or run or do something like that, i have seen a doctor and he told me that i needed to take rest for 3-4 month, but 5 month have ped and nothing changed, please help, how can i get rid of these pain. BTW i man 15