: Well, been a Halo fan for about 10 years, played all the games several times,
: have read most of the books(most importantly just finished the Forerunner
: saga)... I still don't understand, really, how the Flood survives into the
: present(future I guess - 2552). Cortana claims Halo doesn't kill them, it
: kills their food. Silentium seems to suggest they do kill the Flood(along
: with almost all other life). Why is there still Flood on the
: installations? Are they safe havens, like shield worlds? I know they're
: referred to as Fortress Worlds at some point. Did the Forerunner really
: think it was a good idea to keep samples around after how much of their
: civilization was destroyed? Perhaps unwilling to commit genocide? The
: creation of the rings seems to strongly suggest otherwise... I know they
: do reseed the galaxy with many species though. Why is there a Gravemind on
: Installation 05?

The flood spores were kept for research on the rings. They did this because the flood was extra-galactic in nature, meaning that just because the galaxy was wiped clean didn't mean it was gone for good. The spores can presumably live a long time.

ZackDark is correct - the Flood somehow got loose on Installation 05 a long time ago. There was only so much biomass though, enough to build a Gravemind and a decent Flood army, but not enough to overthrow the ring in totality.