-The Forerunners were (or were closely related to) ancient humans, as was heavily implied in Halo 1.
-The Flood were created by the Forerunners, perhaps as a biological weapon. But the Flood got out of hand and the intergalactic plague of zombie aliens destroyed the Forerunners, as was heavily implied in Halo 1 and 2.
-As a last resort, the Forerunners fired their galaxy-wide WMDs - the Halo rings - and starved the Flood to death. Every single Forerunner died in the blast.
-No one knows what the Forerunner looked like, how their society was structured, or the true extent of their knowledge. And no one ever will because unresolved mysteries in fiction can be really cool! Just like mysteries in our own history!

And going unnecessarily further back...

-The planet Earth was in fact the Ark, as was heavily implied by the ending of Halo 2 and made explicit in the leaked Halo 3 script. Oh, and Machiavellian Truth killed the other two Prophets to consolidate his power; he didn't really believe in the Halo rings or the Great Journey.