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Upon reviewing the shear volume of related speculation, we may need to add a "Their Survival" subsection...
Menticided (Menticided@aol.com ) writes:
"The installation was specifically built to study and contain the Flood. Their survival as a race was dependent upon it. I am grateful to see that some of them survived to reproduce."
Perhaps what this means is that the Forerunners and Humans were once allied, and it was the Humans who became infected by the Flood parasites. Maybe the Forerunner believed that almost all of the Human race was infected, and since they were friendly, the Forerunner contained infected Humans to try to find a cure for the parasite and revert the infected Humans back to normal. This could explain why GS is surprised and glad to see Humans, and that they have "survived". The Halo as a weapon serves as a safety measure, obviously, to destroy the Flood, along with all life in the Galaxy. If the Forerunner and Humans were once friendly, this could be why the Forerunner wanted to preserve the Flood, but also be able to destroy them. The Forerunners probably were immune to the Flood for some reason or another [or sufficiently equipped to handle them], which is why they were able to stay alive and build the Halos and such.
And opens another possibility as to why 343 would call you Reclaimer. With Humanity as a partner or client of the Forerunner, the revelation of such a past relationship would still be enough to incite gasps from the audience and yet still leave the Halo universe with all the mystery and aura that only an unknown, powerful, though seemingly dead race can bring.
-Finn
