The easiest way to understand how G-d metes out justice in the world is to compare it to the way any originator of one thing or another interacts with his product. In fact, Ramchal makes a point of underscoring just how symbolic the whole idea of being an “originator” is in the Tradition .
Basing himself on Rambam’s insights, Ramchal points out that aside from their literal meanings, the terms “offshoots”, “products”, or “children” of an originator have all sorts of implications (see Guide for the Perplexed 1:7). They could refer to part of a natural process, as in “Before the mountains were ‘born’ … ” (Psalms 90:2); they could refer to part of a thought process, as in “he …’gives birth’ to lies” (Psalms 7:15); and the like.
Indeed, the idea of “giving birth” to a lie, as in the last example, or to having any idea for that matter is especially illustrative of the point Ramchal wants to make here about G-d’s ways in the world. For, anyone who comes up with an idea that actually produces things is to be credited with everything that results from it. After all, it was he who “gave birth to” — all the latent results of his idea.
But there’s a whole other layer of things to consider here. Because not only should the originator of the idea be credited with having brought all the effects to fruition, he’s also to be credited with having made it possible for the effects of his idea to become perfectly realized — to reach their full potential. And that too touches upon what Ramchal will eventually be driving at, as we’ll see. But first this other point.
As Ramchal words it here, and as we’d learned before , “everything in existence is connected to everything else”, “they each derive from each other”, and “the lot of them are inexorably linked and form a single unit that depends on all of its parts to be whole” and fully-functional.
It follows then that nothing is an isolated phenomenon and that everything has to be considered in its context — as well as by what preceded it and “gave birth” to it, and enables it to achieve its full potential, to use the reference points we made above.
The point of the matter is that each time G-d interacts with the world we’re not only to consider that particular act but everything else connected to it as well, along with everything it could “give birth to”. Because G-d takes all that into account, as well as what might be “perfectly realized” as a result of it, when He acts.
So, while a quite logical and anticipated effect of a particular action might come about in the course of G-d’s interactions, sometimes, and quite unexpectedly, something with deeper implications which is rooted in things beyond our understanding might pop up. And either one might lead to the perfect realization of this or that.
Again, the point is that all of this touches upon some of the things that contribute to G-d’s administration of reward and punishment, and it will go a long way toward explaining Divine Justice in the face of apparent injustice.
 See Klallim Rishonim 22 for this chapter’s Kabbalistic underpinnings as well as R’ Goldblatt’s note 13, and note 61 on p. 485 of his edition; and R’ Shriki’s notes 101-103 (which explain the next few chapters in this light).
 As we wrote, “As Ramchal depicts it in the text, everything in this world functions like a particular piece of a great and mighty clock — from dials, to gears, to screws, to pendulums, etc., all connected, in contact with each other piece, and all functioning in tandem” (3:9:2). Also see 3:18.
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.