I'm also kind of wondering why there's a war going on in the first place? Gears 4 had the same kind of problem, whatever's supposed to establish the conflict isn't explained at all. Why are the humans and the covenant fighting when I'm pretty sure they're both on equal footing and intelligent enough to communicate with each other? Why do the protags in Gears 4 hate living under the COG despite them I think being the good guys in the previous games, and the world having gone to shit? I shouldn't have to look up this kind of basic plot info.
Yeah, Reach while the story is supposed to be a standalone I guess some stuff won't be clear to new players. Hell, for what I remember of Halo CE. It's not clear why the Covenant is at war with humanity (unless you read the game manual). I believe Halo 2 does give more insight of why.
There is a long version and a very short version.
Short version. The leaders of the Covenant (theocracy) declared holy war against Humanity because humans are an offense to their gods. The Covenant have clear superiority in space combat and tech, humans do have a more even and even better performance on ground battles. Humanity is losing the war, hoping for a hail mary of some sort.
Long version. The leaders of the Covenant believe that the creators of all the advanced technology (like Halo) were able to transcend mortality and became gods, and their whole alliance (covenant) is built on that faith that by following their steps they themselves may become gods. There is lots of books behind what actually happened to them, and to be honest it would spoil all the Halo story to explain it further. Even if the games doesn't go as deep. But it would be more precise to say that the covenant leaders declared holy war against humanity to save their own positions of power. The very existence of humanity, if the rest of the Covenant became aware of all the details that the leaders of the Covenant learned, would disprove their faith. And since they are a theocracy.... yeah.