Alright, I'm warning you all now this is going to be a long post. I'm new to the forum, but not new to the theories on Halo. I was around when the cortana letters were making a big deal, though I never bothered to get in to all of that.
My ideas are a conglomeration of a few other theories, but just bear with me.
First I have to rattle off a few things I take as fact.
The Covenant worship the "Forerunners" as gods. Many of the things the Forerunners once had their hands on are referred to as Holy Relics by the Covenant.
"The Covies are imitative, not innovative." This is a direct quote from Halo: First Strike. I take the novels as Halo Cannon - things that have been put down and must be accepted as true. What that quote means is that the Covenant do not invent their own technologies, but rather try to recreate what they find.
There is a definite human-Forerunner connection. Several examples of this connection from the game are, "… a record of all of our lost time. Human history is it? Fascinating." A quote by 343 GS, The Maw. "I scan that battle armor as Class Two, highly ineffective for this style of work. I recommend you upgrade to at least a Class Twelve." 343 GS again, The Library. GS knows a lot about humans and their technology, it would seem. He also constantly refers to Cortana as "the Construct," when Cortana is a highly advanced Infiltrator AI Construct. The final connections I will point out come from the novels Halo: The Flood and Halo: First Strike, respectively. In The flood, Chief touches a control panel and activates a light bridge. Cortana asks him how he knew which button to press. Chief responds with, "I didn't." And in First Strike, when Kelly and Fred hijack two Covenant Wraith Tanks, Fred immediately knows how to operate the tank though he's never seen the inside of one, and has never had any technical readouts in front of him. And since the Covenant have taken all of their technology from the Forerunners, it's safe to assume that the forerunners had something similar, allowing the human-forerunner connection to work in his benefit.
We're gonna go way back in time. The Forerunners are alive and kicking, and have discovered the varied races of the Covenant. They have introduced themselves and have kept their technology to themselves, giving only little bits and pieces of it to the Covenant for various reasons. The races of the Covenant see this technology as the work of magic - or gods.
The Forerunners have, in the eyes of the Covenant, proven themselves to be gods.
Then the Flood breaks out. The Forerunners give the covenant a bit more of their technology and show them how to fight. The covenant becomes a bunch of shock troops for the Forerunners, while the forerunners have their own troops backing them up in special armor. These special troops are called Reclaimers.
The Covenant and Reclaimers begin losing the battle, so the Forerunners construct the ringworlds, hoping to keep the Flood contained within.
The Forerunners herd the covenant to a small part of the galaxy, a tiny corner, and give them what is now known as High Charity..
High Charity, for those of you who don't know, is usually travelling in slipspace, which is like another dimension where faster-than-light travel is possible.
The Covenant are told to remain there with the minimal technology they have while the Reclaimers bring the Forerunners on their last journey. Some of the Covenant don't like the idea of the Forerunners leaving them behind, and are put down by Reclaimers wearing low-level armor. These reclaimers are looked upon by the Covenant as demons, doing the opposite of what their gods do.
The Reclaimers set off the Halos.
Now, there is one more specific thing I must point out.
In The Library, 343 GS says that the Halos are designed to target anything with "sufficient bio-mass and cognitive capability."
For those of you who don't speak geek, here's what that means.
In order for the Flood to live off a host, the host has to be of a certain size, and have a certain level of intelligence.
The stupidity of the Grunts aside, they are still part of a technologically advanced group, and therefore, are converted into carrier forms. (I think it's obvious the carrier forms are from Grunts, because the legs are the same.)
The Covenant and Forerunners who were around for the blast are reduced to nothing but children. Beings too small to actually have any memory of what came before.
The Covenant on Holy Charity, only Elites, Prophets, and Jackals at this point, blame one another for what happened and begin feuding. After a few generations of this war, they happen across Forerunner relics and remember their old gods. They put aside the differences and decide that together, they can find their old gods and what they did on this last Great Journey.
The Forerunners, however, are left with nothing of their old technology. Nothing but a ship known as the Ark, crashed in the middle of a continent on a planet that is much like their homeworld. The Forerunners who survived are all children, too young to have any real memories of life in space. They soon forget it and move away from their crash site in an effort to survive.
A few millenia go by, the Ark is buried by nature and forgotten, and humanity is nearing its old technology. They have re-discovered slip-space and are colonizing planets when the Covenant come across a human outpost. Marines, greeting the Covenant, resemble too much the stories of the Forerunners who, at the last minute, turned on those faithful beings. The Covenant declare a holy war on humanity.
Humanity is overwhelmed, and forced on the defensive. Their innovations bring them closer to where they were than ever before, and the Spartan program is launched. Having secured pieces of their old technology, humans reverse engineer it to create MJOLNIR armor. Mark II.
The rest, as they say, is history.
I told you it would be long.. Didn't realize how long.
But yeah, that's my theory. And if you read it all, you get ten cookies and fifty cool points.