Free will, as all things given to us by God, is good. When it is truly free, and follows the proper contour of its nature and where its nature leads, it will aim for and follow what is good. Free will is a good which leads to that which is good so long as it remains true to itself. The problem of evil lies not in the will, but in its use. When it is allowed to follow through with its natural inclinations, as we see in the humanity of Christ, it will always aim for and achieve what is good, without failure.
When free will is perverted is by when it is taken over by an unnatural mode of engagement, when it is used and subverted away from its natural inclination and someone uses it in order to act, not according to nature, but according to deliberative ends. Free will is good when it is pure and whole, but when it is wounded by an improper engagement, by a person changing the modality of how they will so it is not natural, but individual and mixes good with evil through the deliberative process, the natural good of the will is lost and what a person brings about is a lesser good than should be willed. For, as St. Augustine and so many others have pointed out, when we sin, we deliberate and consider our actions based upon ignorance, and end up going after what we suppose is good instead of willing the actual good. All sin is done in the pursuit of the good, but it misses the mark. Through deliberation, ignorance, bad habits, and the like, we find ourselves not aiming for the true and natural good, but a distortion of that good, a lesser good, which in its defect, causes harm and that harm is what is designated as evil. Yet, because some good is sought after, and there is some element of the good which is accomplished as a result, no matter how deficient the end result, it cannot be said to be pure evil. We can designate it as evil because of what is accomplished through it and the harm that is done, but some good, however little it might be, is accomplished.
This does not mean we can then defend the evil itself because some good remains, but on the other hand, we must acknowledge some good remains for it is the vehicle by which the greater good can once again be found and reestablished. The good which can come out of evil is because of the good which is there after the corruption of evil. As evil and sin resides in the good and corrupts it, the good which remains continues to be good even if it is hindered from being all it should be. It might be difficult for us to ascertain that good, because the sin which we encounter completely overwhelms that good, but we have to acknowledge it has to be there somewhere and hope to use it as a way to once again point to the absolute good which has been lost.
We are all fallen in our ways, and act unnaturally; while at times we might be able to act without thought such as when we drive, so that we act more or less naturally, we still find ourselves constantly in quandaries which leads us to bite off of the tree of knowledge of good and evil and pure an end corrupted by the evil which we have ingested. Such evil contaminates the good, mutating it, causing the end result to be harmful as it disassociates itself from the fullness of the good. Like tooth decay, it produces as it were, a kind of waste product which needs to be cleansed; the decay needs to be removed so that the good which lies underneath it can remain and be made whole once again. The value and importance of penance is that it allows for such purification, and once the person has willfully admitted and disassociated themselves from their own spiritual decay, they can be given the grace needed for them to be made whole; but the grace needs to be applied, the spiritual patient needs to accept the change in their ways for it to take effect, lest the grace itself is lost by repeating the same deeds which caused the spiritual corruption in the first place.
However, there is still the question of the good which was done in the midst of some evil. As it is said God can turn a bad situation around and make a greater good after evil has been abandoned, it must be understood he does this in a way which keeps as much of the good as is possible. This connects with what Jesus accomplished on the cross. He took the sin of the world upon himself. What he can reconfigure from that sin he reconfigures, giving back the good to the person who loaded him with the sin, so that they do not lose anything of the good which they have done. However, as there is spiritual decay, this he takes off from the good and dumps off into the pits of hell, the sewage dump of sin.
This reconfiguration of sin, this finding the good willed in the midst of evil and lifting up that good, complementing it with grace so that the remaining good can once again be put in its proper place in the cosmic order is often left out of discussions on penance. Just as there is no annihilation involved in the transformation of bread and wine into the substance of Christ in the celebration of the eucharist, in penance and absolution, the work of Jesus Christ is to reconfigure the good in the sin so it is made whole instead of allowing the evil behind our sin achieve its nihilistic end. Thus, grace is said to perfect nature, though it might have its sting as it takes the evil and reconfigures it to the good, as medicine often renders someone weak until they are cured of their disease.Rabbi Abraham Isaac Kook had a profound conception on the nature of penitence and its place in the life of each person, as well as society, which can help us understand the work of Jesus much better. The key to understanding penance is it is not to be self-destructive, rather, it must be done in order to cooperate with God and his desire to transform the world for the better. The goal is to bring together all that is good and let it be penetrated by the grace of God, so it can be elevated and turned into something greater than what it was even before it was corrupted by evil. This, however, cannot be done by the negation or destruction of the past, but by the realization of the good within it can have a place in the future as the penitent transforms themselves by God’s grace:
The nature of existence, man’s choice of action and his disposition constitute one chain of being that can never be detached one from another. What mean desires is tied up with what he has done. The deeds of the past, too, are not eliminated from the thrust of life and its basic disposition. Since nothing is totally eradicated the will can impose a special configuration on past actions. This is the secret of penitence which God established before He created the world. I mean to say He expanded the potency of the spiritual life with reference to actions and to existence so that it also embraces the past. The evil deed continues to be reenacted, it causes ugliness and evil, deterioration and destruction, as long as the will did not put a new complexion over it. Once the will has put on it a configuration of the good, it itself becomes a stimulant for good and delight, the joy in God and His light. 
The past is not obliterated but it is able to be reconfigured in God for the greater good. Christians should come to realize that the cross is the altar on which that transformation takes place.
God’s grace is offered to all in a variety of ways. Those of us who are Christians certainly must allow God’s grace be applied to us in and through the work of Jesus Christ, where we see the spiritual alchemy at work, where our corruption is taken over by him and turned into spiritual gold. Those of us who know of the good of confession and can attain to it should do so; those who do not, or are unable to receive it for whatever reason, still have before them the merciful justice of God who will work with them and do what he can for them. We must always leave it up to God as to the result of his work with others. We cannot and must not judge them and say someone will be damned if they die without a clear act of confession and absolution. God is not to be constrained, as St Leo the Great understood:
Suppose that one of those for whom we entreat the Lord fails to receive the gift of pardon here in the world, being cut off by any obstacle whatever, and (having a mortal status) finishes his life on earth before he has access to the remedy prescribed. After he has put off the flesh, he will then be unable to obtain what he did not receive while still remaining in the body. Nor are we required to weight the merits and actions of those who died thus. The Lord our God, whose judgements cannot be comprehended, has reserved for His own justice that which the priestly ministry has been unable to carry out.
The key is to understand God is the judge, not us; we know the mercy and grace possible through sacramental confession. We do not know what is to happen with those who do not avail themselves of that ministry – God is not limited by how he acts toward people, and there can be many reasons why someone would not receive sacramental penance and yet receive mercy and grace and find themselves saved by God. God wants to see everyone saved, and he has shown he is willing to do all that is necessary to reach out and save the world; we cannot know what hidden graces he is giving to others to transform them and bring them into heaven, we just know the normative means he established in the church for us to be transformed. Jesus is reconfiguring sin; that is what we know. Jesus seeks to preserve the fullness of the good and raise it up – he brings the purifying fire of God’s love to the world. What comes of it, we do not yet fully know.
[Image=Confession in a Ukrainian Catholic Church By Водник [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons]
 Abraham Isaac Kook, “The Lights of Penitence” in Abraham Isaac Kook: The Lights of Penitence, Lights of Holiness, The Moral Principles, Essays, Letters and Poems. Trans. Ben Zion Bokser (New York: Paulist Press, 1978), 58.
 St. Leo the Great, “Letter 108” is Pope St. Leo the Great: The Letters. Trans. Brother Edmund Hunt, CSC (New York: Fathers of the Church Inc., 1957), 191.
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