All the species we observe exist because of certain evolutionary traits that have ensured their survival. Far more species have become extinct because of environmental changes or other failures to adapt. Humans are still a fairly young species and there is no guarantee that we will survive, in fact there are many indicators that show we may well nuke ourselves.
Issues of morality eventuality reduce to survivability. In the Christian arena the claimed absolute set of moral rules, if followed, are meant to assure survival in paradise. At a rational level our survival is determined by following actions that are in our best interests; any behavior that is detrimental to other individuals or a group will be quickly isolated by others and the offenders are quarantined or removed from the species. It becomes a matter of survival of the fittest and in human terms that means the ability to think clearly. It doesn’t require religion for us to discover independently that cooperation with others results in mutual benefit and fostering a loving and social environment also assists with our long survivability – these are simply rational determinations that have been part of our evolutionary path and why we have been a success so far.
As for free will – I suspect this doesn’t really exist. Everything appears to be governed by cause and effect in which case every event is deterministic. If we knew every variable in the universe then we should be able predict every future event. However, at the quantum level there is much that appears chaotic and even events that appear to occur before they are caused. Would these events at the micro level be sufficient to create enough randomness to breakup the long change of deterministic cause/effect sequences that has led me to write this cumbersome sentence? And would knowing that free will really doesn’t exist matter? If it is an illusion it seems so difficult for us to determine that who really cares.
As for souls - an interesting fantasy concept not worthy of any serious discussion. All the things that have been claimed as the domain of the soul, e.g. thoughts, emotions, feelings, are all now understood as functions of the brain. As for consciousness and self-awareness - there is no reason to believe that the brain is not also the only and key player in these issues.