Chief would have undoubtedly seen them as he moved about the Shadow of Intent. The lack of them in the game is an intentional oversight done by Bungie for gameplay purposes. Also, the notion that the Chief fighting against Hunters voids the possibility of those with their own opinions and beliefs is absurd.

Still, I'm gonna need proof that they were actually sided with the Elites. Can't just state possibilities as facts.

In Ghosts of Onyx (the section of the book that takes place post-Halo 2), Sangheili lead forces in combat against Jiralhanae and human forces were supplemented by Unggoy, Mgalekgolo, and Kig-Yar forces. Using common sense we could also determine this by the fact that the Covenant is an integrated military and society. Unggoy, Kig-Yar, Huragok, Mgalekgolo, and Yanme'e troops and personnel are going to remain under Sangheili control if they were there to begin with.

"We are aboard, humans, and elites. Will you not come with us brother?" He didn't say Humans and Covenant. And the Post Halo 2 part of GoO was still in the earliest stages of the Great Schism. During that time, yes, Sangheili used Hunters and Grunts as Arbiter did in Halo 2. However, there is no proof that during Halo 3 it was anything more than Elites allied with humanity. And if there were more species, it had to be such a negligible amount that they didn't get mentioned in and "during halo 3 lore"

[i]"There was honor in our Covenant once, and there shall be again!" -The Storm, Halo 3[/i] [quote]He didn't say Humans and Covenant. And the Post Halo 2 part of GoO was still in the earliest stages of the Great Schism. During that time, yes, Sangheili used Hunters and Grunts as Arbiter did in Halo 2.[/quote]You need to keep in mind the context of the situation for the player. It'd be rather confusing to hear that the Covenant is on board when we just defeated them. Those additional forces that sided with the Elites, they aren't just going to disappear, which is what you appear to be claiming. [quote]However, there is no proof that during Halo 3 it was anything more than Elites allied with humanity. And if there were more species, it had to be such a negligible amount that they didn't get mentioned in and "during halo 3 lore"[/quote]There's also nothing that outright says no Unggoy, Kig-Yar, Yanme'e, Lekgolo, or Huragok weren't present as well. I don't deny the majority of Separatist forces deployed on the Ark were Sangheili, but that doesn't void the fact the UNSC technically considered them a Covenant faction, and as the quote above shows, even Thel considered that as well.

It was more bungie didn't want to confuse us in halo 3

Forgot about that line. I suppose that is all the proof I need! Another question. Why were the Brutes in Halo 2 so un armored? During ODST (which was during Halo 2) they were armored the same as they are in Halo 3. So why were there two drastically different armaments for the Brutes that took place in the same time frame?

Part of it obviously comes down to artistic licence and developer constraints. This may offer the explanation you're looking for though: [url=https://www.halowaypoint.com/en-us/universe/species/jiralhanae][i]"Upon integration into the original Covenant body, the Jiralhanae held a number of positions. Some of these jobs were simply an extension of their own native, clan-based organizational structure, though it became more formalized while under the banner of the Covenant. Roles included Chieftains, Captains, Stalkers, Majors, and Minors, all splintered into a number of varieties based on skein, functional and organizational placement, and the point it appeared during Covenant history."[/i][/url]

Idk where I heard it but I thought that the unshaven in armored Brutes were specific to Tartarus' pack. Specially trained to be fearless without armor. But I don't know.