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In the Captain Marvel (2019) film, we learn of the Kree/Skrull war. Later in the film, we see that the Kree are

actually the villains, and have been trying to exterminate the Skrulls, a previously peaceful race. They called them "terrorists" but the film seems to portray this as false propaganda that the Kree use to outwardly justify their genocide against Skrull refugees.

Given that if their official reason is all a lie, why are the Kree actually trying to

exterminate the Skrulls?

Is this ever addressed in the film by anyone?

Through direct and indirect means, we find out of that the Kree-Skrull War is a result of the Skrulls refusing to submit to the Kree. During the reveal, Talos claims that the Kree have been exterminating his people because they did not surrender to the Kree Empire. In confrontations with Yonn-Rogg and the Supreme Intelligence, Carol repeats this claim and neither Yonn-Rogg nor the Supreme Intelligence refute it.

As a result, we can infer that the root cause of the Kree-Skrull War in the MCU is expansionist/imperialist motivations on the part of the Kree.

tl;dr - War is good for business, and in keeping a government in power.

Some history - The Kree-Skrull War is a decades-old plot thread running in the Marvel Comics. In it, the Kree are seen as...well, maybe not the good guys as much as the far lesser of two evils. But the Skrulls are definitely portrayed as evil - they are out to conquer worlds via infiltration, pretty much exactly as portrayed in the movie. From their first appearance in Fantastic Four, the Skrulls are clearly shown to be evil and a destructive force. The war has spilled over to Earth many times over the years, in The Avengers comic and many other places, including, obviously, the various Captain Marvel books. The Kree are certainly the "good guys", but they're still willing to engage in some pretty heavy moves in their desire to win the war.

The change in the movie was (IMHO) to turn expectations on their heads, and to serve as a metaphor for the idea that war, especially very long wars, are bad. Hala and the Kree Empire are seen as very heavy users of propaganda on its people. So having a ready-made enemy in the Skrull "Empire" would be a perfect device to serve the cause of support to the Kree Empire. So the Skrulls are played up as horrific enemies, made easier by their scary "other"ness, and the paranoia-bating idea that they could be standing right next to you. That also allows for increased security over the populace.

Now IMHO, this sort of wastes a classic villain for the MCU (espeically if god willing the Fantastic Four are on their way). But I imagine there's no reason they couldn't concoct some zealous offshoot that would prefer to fight back than to simply run and find a new home. That too could serve as another metaphor for the current world as well, I suspect.