Disclaimer: Microsoft and Bungie own Halo. Joss Whedon owns Buffy/Angel. Stargate is owned my MGM
I own nothing so don't sue me!
The Origin of the Covenant is not what you think young one. For thousands of years we resided in the relative safety of our own universe. We were ruled over by out god Illyria. She had given us life, power and peace. But one day, that would end. Word had come in that an invader was destroying the enemies of Illyria. Normally we would at rejoiced at the mention of that but we didn't. The invader had declared war on all of the Gods.
Under orders from Illyria we began preparing. We built battlefleets, trained soldiers, built weapons and more. But before we were ready they attacked. It was then that we found out who they were. The Ancients.
The Ancients were older then the Forerunner, our saviors and from what we have concluded the Forefathers of the Humans. They attacked and destroyed everything. Only a few of us managed to escape by activating a device left by Illyria. She said that in time of great peril activate it and you will be saved. We did and what remained of us were sent to a barren world on the outskirts of the Ancients home galaxy.
We suffered and toiled on the world for generations before the Forerunners, enemies of the Ancients came. They left what could be called our future, our hope, and our destiny. They gave us the key to space travel.
Over the next few hundred cycles we expanded. Although slowly as the Forerunners never left us with Slipspace technology. After colonization of our 12th system scouts discovered a damaged Forerunner ship. The ship was taken to the space base High Charity where its secrets were revealed. Eventually we incorporated it into the base as its power generation systems were decoded and is now used to power the base. With the data recovered from the ship, we built massive exploration fleets and sent them to explore the space around our homeworld. The first race discovered was the Sangheili.
They were the first to attack, destroying an exploration fleet inadvertedly entering their space. Then when we sent a peace envoy the captured and interrogated the crew. None were alive when rescue came. After that was all out war. Fleets upon fleets were sent into their space and only a few returned. Eventually after a bloody battle the bulk of the Sangheili fleet was destroyed and we offered an ultimatum. Join us or meet your god. Many joined us however some didn't. They met the wraith of the Prophets.
After the pacification of the Sangheili, The Covenant had peace for many years. Whenever war came the Sangheili quickly put an end to it. Next to join us was the Lekgolo, the Hunters. The Lekgolo joined us willingly after we threatened to bomb their world form orbit. At first they were of no use to us but when the Hunagok came.
The Engineers came willingly. They revere technology almost as much as we do the Forerunners and Illyria. So they came, on one condition. They must have access to all our technology. Seeing as this as acceptable the Prophets of the time agreed. We in the Covenant have never regretted the decision. They single-handedly created the armour for he Lekgolo and the plasma weapons we use so effectively against the Humans.
The Unggoy and Kig-Yar were both forced to serve us as our foot soldiers as we realized that the Sanghelli could not perform as infantry in our battles. Since then the Grunts and Jackals have helped pacify thousands of worlds.
On one of these worlds we found out the fate of the Forerunners. They had released a virus, which almost wiped out the Ancients. However the Ancients released one of their own one they found out of this. This creature is said to act like a Flood, washing away anything in a sea of flesh. They fought for years before they realized that they had spread to too many worlds and could not be stopped. They build the Halo's, devices created to destroy them. It worked, the Flood was destroyed and the Forerunners left on a Great Journey to destroy the rest of the Ancients. This is why we follow in their footsteps, to activate the great devices and start on our own Great Journey. But before we can, we must wipe out the remnants of the Ancients and this means destroying the Humans.
For those that don't know, Illyria is the Old One that Fred in Angel was turned into.
But there is another reason for the war with the Humans. Illyria, our God is trapped on their homworld. The Ancients trapped all of the Gods they captured and placed them is stasis devices where they remain trapped. We must free her and take her place at her right hand. We don't know where the Human homeworld is but we will find it.