Derech Hashem – The Way of G-d 1:3:13
In fact, by all rights the soul should actually and quite naturally purify the body to a truly supernatural degree when an individual is born, whether he’s worthy of that or not, given how inherently pure the soul is.
But the point is that G-d purposefully disallowed for that 1, and keeps the soul at bay, if you will, in the course of one’s life, so that His intentions 2 can be fulfilled. So the soul does what it does while it is in the body, and no more, where it otherwise sits stifled and withdrawn, so to speak 3.
It’s also true that the soul should likewise be able to expand and irradiate as the individual engages in good deeds in his life, and to purify the body then to a degree. But that, too, was denied the soul in life.
But those restraints will all be removed in the course of the Resurrection of the Dead, when the soul will purify the body in one fell swoop 4. And the combination of body and soul will grow higher and higher 5 to the degree that accords with the sort of person that individual had come to be in life 6, until they become worthy of the World to Come where they can continue to grow 7.
1 Because of Adam and Eve’s sin.
2 That humans be subject to free will.
3 And it “expresses itself” to a degree in The Soul World as we said in 1:3:11-12. Also see 1:4:2 below and Da’at Tevunot 72.
4 Also see Da’at Tevunot 72, 146-148.
5 See Berachot 17a; Zohar 2:83a, 1:135b; Sha’ar HaGemul.
6 See the end of Ch. I of Messilat Yesharim.
7 Thus it’s written that “Sages have no rest, neither in this world nor in the next” (Berachot 64a). See Emunot v’De’ot 9:10.
See Klallim Rishonim 23 for a lying out of what will happen to the body and soul step by step in the course of the 7th, 8th, 9th, and 10th millennia.
Rabbi Yaakov Feldman has translated and commented upon “The Gates of Repentance”, “The Path of the Just”, and “The Duties of the Heart” (Jason Aronson Publishers). His works are available in bookstores and in various locations on the Web.