Rational man has a spiritual soul. This spiritual soul consists of higher powers and lower powers. The spirit is the higher powers of the spiritual soul. The lower powers are considered the soul. Since our spiritual soul is the substantial form of the body (CCC n. 365), it would be beneficial to understand better passages that indicate a distinction between soul and spirit. For example, St. Paul writes, “May the God of peace himself make you perfectly holy and may you entirely, spirit, soul, and body, be preserved blameless for the coming of our Lord Jesus Christ” (1 Thess. 5:23). He also writes, “For the word of God is living and active, sharper than any two-edged sword, piercing to the division of soul and spirit, of joints and marrow, and discerning the thoughts and intentions of the heart” (Heb 4:12).
Touched upon earlier, the spiritual soul contains both higher and lower powers. The higher powers are often identified as the spirit. The lower powers can be identified as simply — the soul. The higher powers, i.e., the spirit, are intellect, free will (the inner heart), and understanding (the penetration and comprehension of God’s thoughts). The lower powers of the soul direct all the actions of the physical body. The soul allows the body to function as the scriptural mouth of the Human Person. Without the spirit, the soul would be nothing more than an animal soul. However, rational man could never be only a soul. It will always be a spiritual soul. In #367 of the Catechism, it reads,
Sometimes the soul is distinguished from the spirit: St. Paul for instance prays that God may sanctify his people ‘wholly’, with ‘spirit and soul and body’ kept sound and blameless at the Lord’s coming [1 Thess. 5:23]. The Church teaches that this distinction does not introduce a duality [SML] into the soul [cf. Council of Constantinople IV (870): DS 657]. ‘Spirit’ signifies that from creation, man is ordered to a supernatural end and that his soul can gratuitously be raised beyond all it deserves to communion with God” [cf. Vatican Council I, Dei Filius: DS 3005; Gaudium et Spes 22 § 5; Humani Generis: DS 3891].
Thus, the spirit (the upper powers) could never be separated from the soul (the lower powers). It is one indivisible spiritual soul. If that separation were to occur, then the substance of rational man would be annihilated by God (PS., God would never annihilate something He created Good — even if it became corrupted). The unity of the one spiritual soul is vital to this topic. Durrwell writes, “It is there, in our hearts [i.e., the human spirit — SML], in the intimate depths of the believer, that the Spirit chooses his dwelling. In God himself the Holy Spirit of God reaches the ‘depths’ (cf. 1 Cor. 2:10). He is, as it were, the heart of God.” The various powers of the soul are not part of a duality. Thus, the Spirit’s dwelling in the inner heart (the spirit) would inescapably produce a profound impact on the entire spiritual/rational and physical composite human nature. The different powers exist within one single undivided spiritual soul. Whatever affects the spirit (upper powers) equally affects the soul (lower powers). Free will does not reside solely in the spiritual soul’s mythical quadrant (A). Nor does the intellect exclusively dwell in a mythical quadrant (C) of the spiritual soul, and so on.
 Francois-Xavier Durrwell, Holy Spirit of God (original English translation published by Geoffrey Chapman, a division of Cassell, Ltd., 1986; reprint published by Servant Books, Cinncinati, OH, 2006), 36-37.
 cf. St. Hildegard of Bingen, Scivias (Mahwah, NJ: Paulist”Press, 1990), 35.
 cf. Rev. Edward Leen, The Holy Spirit, (New York, NY: Sheed & Ward, 1939; Sceptor Publishers, 1998, 2008), 32-33.
 Catherine of Siena, The Dialogue, 32, 103-104, 277.