Section 21 of John Locke's 2d Treatise on Government: “On Civil Government” has remarkable resonances with the Chinese idea of the "Mandate of Heaven." This idea maintained that while the imperial Chinese government maintained the Mandate of Heaven by wise rule it was the legitimate judge over its subjects. But when the imperial Chinese government misbehaved, it lost the Mandate of Heaven; attempting to obtain justice then required war. the previous Section 20, which I discussed in "If the Justice System Does Not Try to Deliver Justice, We Are in a State of War," talks about a government misbehaving. Section 21 then contrasts society under a reasonably just government and a state of war in which one hopes for justice from military victory:

To avoid this state of war (wherein there is no appeal but to heaven, and wherein every the least difference is apt to end, where there is no authority to decide between the contenders) is one great reason of men’s putting themselves into society, and quitting the state of nature: for where there is an authority, a power on earth, from which relief can be had by appeal, there the continuance of the state of war is excluded, and the controversy is decided by that power. Had there been any such court, any superior jurisdiction on earth, to determine the right between Jephtha and the Ammonites, they had never come to a state of war: but we see he was forced to appeal to heaven. “The Lord the Judge (says he) be judge this day between the children of Israel and the children of Ammon,” Judg. xi. 27. and then prosecuting, and relying on his appeal, he leads out his army to battle: and therefore in such controversies, where the question is put, who shall be judge? It cannot be meant, who shall decide the controversy; every one knows what Jephtha here tells us, that the Lord the judge shall judge. Where there is no judge on earth, the appeal lies to God in heaven. That question then cannot mean, who shall judge, whether another hath put himself in a state of war with me, and whether I may, as Jephtha did, appeal to heaven in it? of that I myself can only be judge in my own conscience, as I will answer it, at the great day, to the supreme judge of all men. 

Does Good Win in the End?

But let's take a look at the idea that military victory is positively correlated with justice. If a benevolent God does not yet exist, then this requires an argument. 

Martin Luther King said, memorably, 

The arc of the moral universe is long, but it bends toward justice.

Quote Investigator identifies antecedents of this saying. Unitarian minister and Transcendentalist Theodore Parker published an 1853 volume of sermons with this passage:

Look at the facts of the world. You see a continual and progressive triumph of the right. I do not pretend to understand the moral universe, the arc is a long one, my eye reaches but little ways. I cannot calculate the curve and complete the figure by the experience of sight; I can divine it by conscience. But from what I see I am sure it bends towards justice.

Things refuse to be mismanaged long. Jefferson trembled when he thought of slavery and remembered that God is just. Ere long all America will tremble.

and Morals and Dogma of the Ancient and Accepted Scottish Rite of Freemasonry, copyright 1871 had this passage:

We cannot understand the moral Universe. The arc is a long one, and our eyes reach but a little way; we cannot calculate the curve and complete the figure by the experience of sight; but we can divine it by conscience, and we surely know that it bends toward justice. Justice will not fail, though wickedness appears strong, and has on its side the armies and thrones of power, the riches and the glory of the world, and though poor men crouch down in despair. Justice will not fail and perish out from the world of men, nor will what is really wrong and contrary to God’s real law of justice continually endure.

In the absence of the supernatural there is still one reason that history is tilted toward victory of good over evil. Those who can cooperate with others who are unlike them can form larger coalitions than those who can only cooperate with others similar to them. The strategy of cooperating with others who are similar can be pushed a long way: each of us is built around a collection of genetically near-identical cells, with reproduction monopolized by a few germ-line cells much as beehives are built around collections of genetically closely related individuals with reproduction monopolized by the queen bee and the drones. But assuming that strategy of cooperating with similar individuals is pushed to the limit on both sides of a conflict, the side that can also manage cooperation among unlike individuals or unlike groups of individuals will have a big advantage. While not all the way there, the ability to cooperate with unlike individuals or groups of individuals is one step toward agape, the kind of love the early disciples of Jesus talked about. 

But far short of reaching a high form of love, the victory of those with a greater ability to cooperate with unlike individuals can bring progress that merits being described as a victory of good against evil. I have in mind the decline in violence over the course of history that Steven Pinker writes about in The Better Angels of Our Nature—a book I highly recommend. 

In any individual battle, evil (however defined) may win, but the dice are loaded in favor of goodness that is associated with an ability to cooperate with those who are different.

Conversely, the dice are loaded against those who cannot cooperate with those who are different from them. Hitler provides a good example. Because Hitler was not willing to cooperate with Jews, Nazi Germany lost access to scientific talent important for the war effort. Because Hitler could not cooperate with Stalin, he had to fight a two-front war. Because Hitler could not cooperate with Slavs whom his troops liberated from Stalin, he could not consolidate his hold on the Ukraine as well. If Hitler had not let ideology get in the way of the war effort he led, he would have been more likely to win. But if he had not been motivated by ideology, things might not have gotten to that point in the first place. 

This may not be as much to hang one's hat on in hopes for the victory of good over evil as one might wish, but other than my unfounded native optimism, it is all I have.