At night and early morning my feet are in severe pain especially on the lateral sides. initially pain started in knees . what could be the reason?

Sometimes: plantar fasciitis can cause pain in feet. will need to see podiatrist for proper dx

Chicken or the Egg.: Since the pain initially started in the knee, there is a distinct possibility that the problem is in the knee. The feet may be involved only as a referred or compensatory pain. To relieve the knee pain, you change the way you walk, thus changing the way your feet normally work. A thorough lower extremity evaluation may be necessary to find the real culprit, the knees or the feet.