Thus we are carried far beyond Greek thought, whether it be Plato's or Aristotle's. For if the human soul is a substance and principle of substantiality, it is because it is an intellect, that is to say an immaterial being by definition and consequently incorruptible. After that, St. Thomas can turn to his own account, and does so unweariedly, the famous Aristotelian principle that the individual exists for the sake of the species; only, by a now inevitable reversal, the consequences that favoured the species in the Aristotelian system work out in favour of the individual in the Christian system. That to which the intention of nature now tends is much less the species than the incorruptible. If, sometimes, it looks to the good of the species rather than that of the individual it is only in those cases where the individuals are corruptible and the species alone endures; but in the case of incorruptible substances, it is not only the species that permanently endures, but also the individuals. And that is why the individuals themselves fall within the principle intention of nature: etiam individua sunt de principali intentione naurae. Now it is the soul that is the incorruptible part of man; and consequently we must admit that the multiplication of human individuals is a primary intention of nature, or rather of the Author of nature, Who is the only Creator of human souls: God.
With respect to species in which the individuals do not endure, the individual exists for the sake of the species. The end of the individual is the perpetuation of the species. But in species in which the individuals are incorruptible (i.e. eternal) we have the paradoxical situation that the individual himself is an end in himself; even more than this the end of the species is not merely itself but the individuals. Gilson is making a philosophical point here; the immortality of the human soul is known through philosophical analysis, not merely revelation (although Christian revelation may have provided the initial motivation to pursue this line of philosophical investigation.) That the species man exists for the eternal individual man is a principle of nature, and can be known through nature; it isn't something imposed on nature through an arbitrary act of God's will.
But what happens when the immortal nature of man is lost to view, as it has been in the modern world? Then, inevitably, the relationship between the species man and the individual man will change, or rather, it will be perceived differently. There will no longer be a rational basis for holding the individual man to be an end beyond the species. Like every other species, the individual man will come to be seen to exist for the sake of the species, as the individual dog exists for the sake of its species. It's not hard to see here the foundation for the horrors of the twentieth century, where millions of individuals were sacrificed for the material progress of humanity (in Communism) or for pseudoscientific biological progress (as in Nazism). Those horrors have tempered the ambitions of secular man, but the immortal nature of man is still no longer in view anymore than it was in the past century; so while we may not be in immediate danger of twentieth century style mass atrocities, it may be expected that the current century will provide novel assaults to the dignity of the individual man.