So there are a number of Halo/Stargate crossovers, most where a single ship is displaced into a different universe and the impact they have there...

But what if they are the same universe?

Five million years ago a plague swept across the Milky way galaxy, the Alterans, helpless to stop it create and fire the Dakara device - a machine that uses the stargates seeded throughout the galaxy to propagate an energy wave throughout space that destroys life.

The few uninfected Alterans flee to the Pegasus galaxy before the galaxy, leaving Earth to be reseeded with life similar in form to themselves - Humans.

One million years ago Precursors arrive in the Milky way and find the stargates, what they see as a destructive influence on lesser species developments, and so they collect the stargates and allow the galaxy to evolve in a more natural progression, in accordance with their desires.

One-hundred-thousand years ago Humanity is a galactic power along with their San'Shyum allies - however, their heavy handed and desperate handling of the Flood threat has earned them enemies of the Forerunners, an equally (if not more) advanced and more numerous force. War ensues and when the Forerunners are victorious they devolve humans and leave them stranded hunter gatherers on their home planet. Humans as a last vengeance destroy the cure they developed for the flood.

When once again the flood become a threat the humans and San'Shyum are no longer there to face it and the Forerunners are slowly losing. A device is discovered that proves more effective in destroying the flood than any other, however, the device destroys indiscriminately leaving nothing biological living. In their study of the Dakara device the can find no way of targeting the living flood without destroying all other biological systems. They scale up the device - the original Dakara device being incapable of effecting a large enough region without the stargates. The Halo array is created and when defeat is assured, fired. Once more destroying all life in the galaxy. Seed ships set out from the Ark to reseed the galaxy with the life the Forerunners were forced to take...

Or at least that's what would have happened if one LifeWorker of the Forerunner hadn't discovered something odd about one of the species being catalogued for the reseeding.

It was a small aquatic life form, though possessing minimal cognitive function of its own, or really anything seemingly noteworthy at first glance, the genetics catch her attention - there is something about it that seems artificial. This Forerunner has discovered the Cure, thought destroyed by the humans, but really only hidden. This Forerunner has discovered the Goa' uld.

(I mean if you really think about it, here's an organism that wraps around your spinal cord and gives you an incredible ability to heal, a longer life span, and better memory - it's even a well known fact of the stargate universe that the goa'uld are very well suited to taking humans as hosts - what if that was by design? what if humans designed them to protect them from the flood?) - (when you think about it, goa'uld are small animals with tiny brains, while genetic memory is well and good you can't actually think with genetic memory, only remember - so it seems entirely possible to me that the original goa'uld didn't have personalities or anything of the sort, but that that developed over the 85,000 years between the firing of the halo array and the stargate story... after all when symbiotically matching up with hundreds if not thousands of animals and unas, one must build up an immense repository of genetic memory that could easily overwhelm the lesser experiences of a short lived species)

Anyway in this story the Forerunners discovered the Cure and with their own incredible sciences were able to adapt it to their own physiology, almost immediately there is a turning of the tides in the unending battle against the Flood. Slowly but surely the flood are pushed back and quarantined - a single halo firing, reaching only three percent of the galaxy, but destroying the final dregs of the Flood - including thousands of ships who were attempting to flee the galaxy entirely and were already thousands of lightyears into the galactic void.

The Forerunners, greatly weakened, but triumphant begin to recover...

A/N the story can go almost anywhere from here... however, I imagine that the Alterans aren't such pussies as they are in stargate and put down the wraith like the insects they are... eventually a number of Alterrans decide to return to the milky way to see what has become of it - expecting that by now the humans will have matured into a powerful spacefaring empire... they're horrified by the crimes the Forerunners have committed against the humans (their legacy) and by the brutish and heavy handed way they rule the galaxy. The alterrans return to pegasus and tell their fellows of the news and...

Well honestly what do you expect - war! in this war it will be the Massive empire of the Forerunners - trillions strong with incredible industrial might (after all these are the beings who build planets in their spare time)

Against the Alterrans a smaller group of only a few billion, who enjoy and understated elegance to their technology, subtle but incredibly powerful - the Alterrans will have the technological edge even if not huge. however, Alterrans never fight infantry and will be completely over run in any sort of ground conflict against the Forerunners...

Anyway that's the idea for the story.