Objection 1. It would seem that the Son of God did not assume flesh through the medium of the soul. For the mode in which the Son of God is united to human nature and its parts, is more perfect than the mode whereby He is in all creatures. But He is in all creatures immediately by essence, power and presence. Much more, therefore, is the Son of God united to flesh without the medium of the soul.
Objection 2. Further, the soul and flesh are united to the Word of God in unity of hypostasis or person. But the body pertains immediately to the human hypostasis or person, even as the soul. Indeed, the human body, since it is matter, would rather seem to be nearer the hypostasis than the soul, which is a form, since the principle of individuation, which is implied in the word "hypostasis," would seem to be matter. Hence the Son of God did not assume flesh through the medium of the soul.
Objection 3. Further, take away the medium and you separate what were joined by the medium; for example, if the superficies be removed color would leave the body, since it adheres to the body through the medium of the superficies. But though the soul was separated from the body by death, yet there still remained the union of the Word to the flesh, as will be shown (50, 2,3). Hence the Word was not joined to flesh through the medium of the soul.
On the contrary, Augustine says (Ep. ad Volusianum cxxxvi): "The greatness of the Divine power fitted to itself a rational soul, and through it a human body, so as to raise the whole man to something higher."
I answer that, A medium is in reference to a beginning and an end. Hence as beginning and end imply order, so also does a medium. Now there is a twofold order: one, of time; the other, of nature. But in the mystery of Incarnation nothing is said to be a medium in the order of time, for the Word of God united the whole human nature to Himself at the same time, as will appear (30, 3). An order of nature between things may be taken in two ways: first, as regards rank of dignity, as we say the angels are midway between man and God; secondly, as regards the idea of causality, as we say a cause is midway between the first cause and the last effect. And this second order follows the first to some extent; for as Dionysius says (Coel. Hier. xiii), God acts upon the more remote substances through the less remote. Hence if we consider the rank of dignity, the soul is found to be midway between God and flesh; and in this way it may be said that the Son of God united flesh to Himself, through the medium of the soul. But even as regards the second order of causality the soul is to some extent the cause of flesh being united to the Son of God. For the flesh would not have been assumable, except by its relation to the rational soul, through which it becomes human flesh. For it was said above (Question 4, Article 1) that human nature was assumable before all others.
Reply to Objection 1. We may consider a twofold order between creatures and God: the first is by reason of creatures being caused by God and depending on Him as on the principle of their being; and thus on account of the infinitude of His power God touches each thing immediately, by causing and preserving it, and so it is that God is in all things by essence, presence and power. But the second order is by reason of things being directed to God as to their end; and it is here that there is a medium between the creature and God, since lower creatures are directed to God by higher, as Dionysius says (Eccl. Hier. v); and to this order pertains the assumption of human nature by the Word of God, Who is the term of the assumption; and hence it is united to flesh through the soul.
Reply to Objection 2. If the hypostasis of the Word of God were constituted simply by human nature, it would follow that the body was nearest to it, since it is matter which is the principle of individuation; even as the soul, being the specific form, would be nearer the human nature. But because the hypostasis of the Word is prior to and more exalted than the human nature, the more exalted any part of the human nature is, the nearer it is to the hypostasis of the Word. And hence the soul is nearer the Word of God than the body is.
Reply to Objection 3. Nothing prevents one thing being the cause of the aptitude and congruity of another, and yet if it be taken away the other remains; because although a thing's becoming may depend on another, yet when it is in being it no longer depends on it, just as a friendship brought about by some other may endure when the latter has gone; or as a woman is taken in marriage on account of her beauty, which makes a woman's fittingness for the marriage tie, yet when her beauty passes away, the marriage tie still remains. So likewise, when the soul was separated, the union of the Word with flesh still endured.
Source: Summa Theologica (New Advent)