: 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?

Flood specimens were mentioned in Halo CE to be stored on the Halo ring. The had to have been placed in containment that would survive the Halo effect.

That line by Cortana was more to mention the Halo weapon doesn't discriminate what it destroys in that fashion. When she says 'Halo doesn't kill Flood', interpret it as 'it doesn't [i]only[/i] kill them' because she goes on to elaborate that humans and Covenant are susceptible to the effect too.

Delta Halo also had stored samples of Flood. In some of the literature, such as The Smuggler, it's suggested that containment failed. Although it's commented that Delta Halo's monitor was 'lax in the areas of maintenance and security', since 2401 Penitent Tangent was captured by the Gravemind, it's likely it was seized by the Flood during their containment outbreak and not permitted to try and enact protocols to clean it up and contain the outbreak. I doubt he was lazy and that allowed the breach...I think it simply occurred and he couldn't then stop it once the Flood got out. He's quite frantic in Halo 2 when he observes that protocol has not been met and he's still in the clutches of the Gravemind.