It is not what enters a man that defiles him, but rather what comes forth from his heart that harms him. (Matt 15, 11-19) It is by the fruits that spring forth from our hearts that we are going to be judged. With this in mind, we should look into how these evil seeds get planted in our hearts and minds in the first place.
Today's Gospel instructs us that the enemy has spread these weeds in our souls while men were sleeping. The devils, the world, the concupiscence of our fallen natures are all our enemies. We give these enemies access to our souls when we overindulge through gluttony or when we are careless and lazy. We must always be on our guard (never sleep spiritually) when it comes to avoiding the occasions of sin. When our bodies are over-indulged, they begin seeking sinful indulgences and pleasures, our resistance is down and so, we become easy prey to the enemies of our souls. One fault or failing leads us forward to even greater faults and sins.
The angels in Heaven see clearly the weeds (evil thoughts and desires) after they have taken root in our souls. These are ready to do the will of God and ask if they should pull them out. God does not allow this lest in rooting out the weeds, the good grain should be destroyed also. It is often this patience of God that causes us to pause or wonder about the Divine Will. We often hear things like: "Why does God allow this?" "Why does God not do something about this?" "Why does not God just strike him now?" God is patiently waiting for the time of harvest.
There is often a grain of goodness that is to be saved even in the worst of sinners. God did not destroy Esau because He foresaw that the saintly Job was to one day descend from him. God did not call forth the destruction of the tax collector Matthew, because He knew that He would one day become a great Apostle. He did not strike out Saul, because He was necessary to bring the Gospel to the ends of the earth.
We often may consider that even the evil in this life provides help or assistance to the good. While it generally happens that good parents have good children; history also records good children coming forth from not-so-good parents. We also see that evil shopkeepers may provide the necessities of life for good people. There is even a spiritual benefit if we look deep enough. Bad people give good people the occasion or opportunity to practice patience, long-suffering, and many other virtues that could not otherwise be practiced and developed. Thus, it is that bad people do some good even in spite of themselves.
God has a way of drawing good, even from evil. This in no way condones the evil or makes it good. For example: Jesus has instructed us that scandals are necessary. (They strengthen the good and help them to advance in grace.) But, He also says "woe to those by whom the scandals come." (St. Matthew 18, 7) We must hate evil and resist it to the best of our abilities so that it does not take root in our souls, but we must, likewise, patiently bear with the evils we find around us and, in this manner, advance in grace.
We find that Jesus instructs us: to turn the other cheek; to not render evil for evil; even to love our enemies. We must do good to those that do evil to us. We must bless and not curse.
In examining ourselves, we should begin to see that evil thoughts arise within us because an enemy has planted them there. He was able to plant them there because we were not on guard and protecting our hearts and minds from evil influences. We should not have become careless and should have avoided the occasions of the temptations that lead to these thoughts. We can blame the enemy, but we must also blame ourselves for allowing the enemy access to do his evil deeds. Let us not despair when we see our hearts and minds filling with evil thoughts. What are we to do?
Psychologically, if we work to directly remove these thoughts, they only tend to become even more embedded in our minds. Just try telling yourself not to think of something. At that very moment you begin to think of exactly what you decided not to think of. This head on, or direct approach does not work. We are best off, if we leave them alone for the time being. There will come a time when they will be gathered up and burned. For now, the best thing to do is to focus upon the good seedlings (the good thoughts) it is best that we work on cultivating and nurturing these.
We must obviously repent and confess our evil thoughts if they are serious sins, but then we should direct out thoughts to good things, and not dwell upon the evil ones. The very thought of sin often causes more sin. The thoughts of virtue often lead to even more thoughts of virtue and eventually to the very practice of virtue.