Okay, there's a fair amount of people that believe the Halo series has no plot, or, rather, has a generic Scfi-fi plot. This puts Halo into the same category as, say, Gundam Wing (seriously. what the hell).
I have heard references to other games (Timesplitters, MGS, Half-Life), which, the people claim, have more thought put in to them and their backgrounds.
Bungie spends a lot of time developing games not only because they want them to be pretty, but because of the extreme amount of importance they place on details.
For example http://halo.wikia.com/wiki/Gravemind
(yeah, spoilers, it's a wiki) I was unaware that the Gravemind occasionally spoke in Trochaic Heptameter.
I also missed pretty much all of the terminals on my first run-through of Halo 3, which means that I missed a whole lot of backstory involving the Forerunners and an A.I., none of which is mentioned anywhere else.
I haven't bothered to read the Halo novels, which are supposed to be an expansion of the Halo Universe, a highly coded and complicated Universe in its own right.
There are a lot of loose ends left around after Halo 3, and I am excited to see what will happen next. The Flood still pose a menace on par to Star Trek's Borg (and I guess, meh) Stargate's replicators, and there are likely Flood organisms elsewhere. It is highly possible that they have conquered other Galaxies, or (this would be neat... in a horrifying sort of way) have infested every other part of visitable space/reality.
Unlike the Borg, however, the Flood have yet to be Deus-Ex'ed to senility, and have quite a bit of narratological importance left.
So, I am excited about where Bungie will take Halo. Not as excited as I am about Battlestar Galactica, but that's a different subject.
Er, and I apologized for the post sounding so rushed. I will try to clarify (and will probably retract or add statements) as responses come in.