Thoughts come out from pure consciousness due to the faculty of consciousness called imagination (maya). Since one thought is separate from another thought from the perspective of individual thought, there is manyness. Every thought is a separate thing/being from this relative standpoint. However, each thought is made of consciousness itself and hence what appears to be many from the perspective of an individual thought actually is one from the perspective of consciousness.
Let us say that there are 5 eatable items placed at the dining table during lunch that A is having. From the perspective of A, he has 5 choices and he can choose to eat whatever he wants to eat out of these items. In this way, A has limited free will.
However, the choice that A makes to eat something is governed by the thoughts coming out of A’s mind. These thoughts come out due to the laws of nature of which A has no control. Thoughts automatically come out of the mind, processed by the intellect and the decision is made. All these things happen automatically. In this way, free will is not really free as laws of nature govern both the origin & processing of thoughts.