The soul is a substance that is distinct from the body yet totally integrated with it. It is totally different than anything material. Paul tells us, What is a man profited, if he shall gain the whole world, and lose his own soul? Or what shall a man give in exchange for his soul? (Matt 16:26) Also, Fear not them which kill the body, but are not able to kill the soul (Matt 10:28).
The word soul (ψυχή psychē) in Greek means life or vital breath, so we might think of it as the breath of God that God breathed into man when he was made and given life. Saint Gregory the Theologian says that the soul is the breath of God, and while being heavenly, it endures being mixed with what is of the dust. It is mixed like the yeast is with flour to form bread. At death the body and soul temporally separate, but this is not a separation forever. At the General Resurrection we will arise in a new renewed form uniting body and soul.
Basically, how the soul originates in an individual is not known, but remains a mystery. We do know that it does not preexist as in the philosophy of Plato. The Church has rejected this view.
Soul is immortal
The soul is immortal and this is one of the most fundamental aspects of our Christian faith. This view predated the New testament times. Then shall the dust return to the earth as it was, and the spirit shall return to God Who gave it. (Eccl. 12:7) Jesus often pointed to the immortality of the soul as the foundation of a pious life. He condemned the Saducces, who denied the immorality of the soul.
For me …to die is gain...having a desire to depart, and to be with Christ (Phil 1:21,23). For we know that, if our earthly house of this tabernacle were dissolved, we have a building of God, a house not made with hands, eternal in the heavens. For in this we groan, earnestly desiring to be clothed upon with our house which is from heaven (II Cor 5:1-2).
Soul is meant to govern the body
From the early Church Fathers we learn that it is characteristic of the soul to govern the strivings of the body, and characteristic of the body to accept this governance. The apostle Paul said that the "body wars against" the soul, and that "I buffet my body", to keep it under control. It is like the body is the tool of an artist and that artist is the soul. It is not a natural condition for the soul to be subject to the impulses of the body. The soul is capable of entering into warfare with the strivings of the body as if it is something foreign to it and hostile to it and able to gain victory over it. Our present condition is a difficult and unnatural one as the body is in control of the soul and the soul is separated from God as illustrated on the left in the diagram below. This is far different from the natural condition shown on the right where the Soul is in harmony with God and directs the body.
This is our major challenge and responsibility to ask God to help our soul regain its control over the bodily demands. The sacraments of the Church help us in this task. Of course we must first recognize this condition and have sufficient humbleness to ask for God’s help and forgiveness.
In Genesis we learned that man was created in the likeness and image of God. Scripture only says that man was created “in the image of God” but does not tell us what part manifests this image. Some see it as reason, others as free will, and others immortality. It may well be all of these. But since we know that God is not clothed by a kind of body like our flesh and bones, this image of necessity resides in the our soul.