When discussing concepts and themes in Faust it is critical to remember that the Urfaust, or original Faust, was published in 1775 and came immediately after Goethe's success with The Sorrows of Young Werther (1774), which is the story that launched Romanticism. The Urfaust espoused the same Romanticist sensibilities that Werther expressed. However, Goethe rejected Romanticism soon after having initiated it.
Following his move to Weimar, Goethe adopted Classicalism. Thus the revised Part I (1829)--(which followed the Faust Fragment in 1790 and a completed Faust Part I in 1808)--and Faust Part II (1832) reflect Classicalist concepts, not Romanticist concepts. This is important to understand because themes emerging from these differing concepts will, of necessity (and author intent), be different. Although it is true the inclusion of the Dedication, Prelude, Prologue do something to unify the disparate parts, concepts and themes (whether there is thematic or other unity in Faust has long been a contested critical debate).
One unified concept introduced in the Prologue, evident in Part I, and carried to fulfillment is Part II is the concept of mutability (changeability). Goethe's concept is that while all things are mutable, or changeable, they are mutable only within certain bounds. His horticultural studies of mutability in plant life solidified this concept, first evident in the Urfaust ("Night") and still evident in the last pages of Part II ("Mountain Gorges, Forest, Rock, Desert").
Faust: I feel ready, free
To cut a new path through the ether
And reach new spheres of pure activity. 705 ("Night")
The Mater Gloriosa: Come! Rise towards the higher spheres!
Gaining awareness ... he will follow. 12095 (V.vii)
The theme related to this concept of mutability within limits is that "a good man" will triumph over temptation in the end and continue to be good:
God: A good man, in his darkest yearning,
Is still aware of virtue’s ways. (Prologue)
It takes Faust a long time to do so, but he embraces good and "what Men need" (IV.i). He turns his attention to building a safe harbor that will feed and protect "millions." Further, after his Act V.v "Midnight" visit with Care--whom Goethe initially introduces in the Urfaust in "Night" ("Care has nested in the heart’s depths, / Restless, she rocks there, spoiling joy and rest, 645)--he renounces magic and his quest for forbidden knowledge. Thus he fulfills the theme of goodness by reversing the direction of changeability in his life and by thus restoring his goodness. This is as God predicted it would be, because Goethe's concept is that mutability has limits, a concept that goes badly for Mephistopheles:
Mephistopheles: Now with what they’ve salvaged from the tomb,
As their own prize, they’ve flown off to heaven:
They’ve stolen a great, a unique treasure:
That noble soul, mortgaged to my pleasure, 11830