Free Will
My hypothesis is that the appearance of free will may simply be the interaction between lower and higher states of consciousness.
The rational moral self, driven by deep thought, and the irrational emotional self, driven by core bodily functions.
These two minds influence each other and sometimes clash.
The higher self might have other considerations, ideals, morals, wants and needs than the lower self.
There is a struggle between the two "selves", and this gives rise to us needing to make a conscious decision.
Sometimes when there is a disagreement between the two, and the lower self wins, we may feel guilty about it because the higher self disagrees with the decision, but was not able to prevent it from happening.
It's simply put a highly complex tug of war between two states of ourselves, and our actions are influenced by the physical world we live in and what we experience, as well as our internal bodily functions (e.g. hormones such as testosterone, estrogen, dopamine, serotonin etc).
The lower self is at the very core of our physical existence. It doesn't necessarily require consciousness at all to make decisions, it's purely emotional and instinctual, driven by our body's chemistry and its interaction with the world.
Remove the higher self, and you (possibly) remove consciousness altogether. You would still function in the world, just like a sleep walker can still do complex things without knowing about it, but there would be no "clash of wills" occurring anymore, since the opposing party has been removed. You (the physical human animal) would be free to do whatever without any moral implications.
The higher self is the next step in our evolution, probably (at least partially) brought on by the emergence of civilization and the new and more complex concerns it brought with it. It, too, is purely physical, but (not to be taken literally) is built on top of the already existing lower self. Not unlike modular software that has basic core code with more advanced functions built on top of it, the higher self takes a lot more into consideration when making decisions than does the lower self.
When, for example, we are in an unstable mental state because of stress or depression, the higher self isn't able to function as well. This, in conjunction with hormonal fluctuations in the body, can make us do or say things that we would otherwise not. If we are kind and considerate in our stable state, ruled mostly by our higher self, we may suddenly become mean and inconsiderate when our internal environment changes and the lower self takes over, sometimes completely. When suffering from high anxiety and depression we may not be able to think or act rationally at all.
Free will, if defined as being able to make decisions without being strongly influenced by our human nature and the world around us, simply does not exist.
Beyond the Physical Realm
Even though our entire existence is based in the physical reality of our universe, and ruled by its laws, many humans have a sense that there is something more. Maybe other animals have such a sensation as well, but since we're not able to communicate with them it's impossible to know for sure (at least with the knowledge and methods of today).
Bringing forth the feeling of being in touch with a higher being has been demonstrated in the lab by stimulating certain areas of the brain. So, yes, there is a part of the brain that actually makes us "feel the presence of God".
Atheists have of course precluded that this is evidence that God exists only in our head, that there is no higher being at all. It's just a function of our consciousness. While this may well be the case, the many events that people have experienced in conjunction with such feelings of the presence of a higher power goes entirely unexplained by this. Highly unlikely things that occur at precisely the right time while simultaneously experiencing this sensation.
Religions have tried to define what this higher being is. In singular or plural form as well as no form at all. My own highly personal opinion, which this writing is nonetheless an expression of, is that yes, there is something more to reality than what we can see, feel, hear, touch or measure.
But my conclusion throughout the years of spiritual searching, learning about many religions, including obscure and all but forgotten ones like Zoroastrianism, is that trying to define "God" is an exercise in futility. I don't believe any one religion holds all the answers, and many of them are also riddled with tribal politics and prejudice commonly accepted at the time.
It's also, in my opinion, proven that religious texts all got the creation story wrong. Not a single religion was able to accurately describe in a scientific fashion the creation of our planet or the universe. Many of them even got the order of events completely wrong, and they all have a very simplistic and human centered explanation that's not at all in touch with reality.
All that said, I still believe that this doesn't take anything away from the experiences of the people that created these religions. They all had spiritual events happen to them, and they all learned something that they wanted to share with the rest of humanity. As a citizen of the Western civilization, I can't help but notice how many of our laws and morals today are highly influenced by the teachings of Jesus. The ideas that he and his followers brought into the world and spread across the globe changed the way that we think and act towards each other.
I sincerely believe that Jesus was a very spiritually gifted person, and that he did indeed have a connection to what we choose to term "God". He was of course also heavily influenced by the Jewish tradition and thus chose to frame his beliefs and experiences in such a way that it made sense both to himself and the people around him that he wanted to teach. But many of his values were unique at the time, and went against much of what was currently the norm.
I choose to call myself spiritual, but not religious. I can read religious texts and see them in the light of the time and place they were written, and for whom they were written for, and still take the lessons given therein to heart. I can also have a personal relationship with "God", without trying to define what "God" is or what "God's will" is.
I feel that this has given me the freedom to express my thoughts and feelings to that higher power without fear. I can question everything, including the omnipotence of said being, without ever jeopardizing my spiritual relationship. It's a very honest and open friendship. I give thanks when it's due, but I also don't expect miracles. There is an order to things, and for whatever reason, everything that happens does so for a reason. Good or bad.
Keeping my mind entirely open, accepting that I will never fully understand "God", has made it easier to not wonder why so many horrible things are allowed to happen in the world without any divine intervention. It doesn't matter to me if "God" is omnipotent or not. God is my life-coach, and my dear undefined friend. Demanding perfection from friends is never a good idea.
Putting It All Together
Even if we humans on this planet are nothing but sophisticated conscious modular software without any real definite free will, and "God" is but our programmer(s), what does it really matter? We still have to make decisions every day, and we are still very much conscious and aware. We still feel, we still experience and learn, and we can still grow our relationships with our programmer(s).
And maybe, just maybe, that relationship can lead to true free will, and an existence beyond this short lifetime. Who knows? I sure don't. And not knowing is what makes life an adventure.