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If all sentient life (including humans) in the galaxy was intact, it means that Halo array was silent for long which means the Flood wasn't a threat to galaxy for long. Its only possible for alive Flood (wherever they are) if they were locked out like they were in Halo installation 04.

How could Flood type dangerous race be captured?

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The Forerunners probably took samples of spores for investigation after battles, or during sterilization. They also had to fight a Gravemind on one of the Halos (see Halo: Primordium) which would have provided abundant research samples.

You're also underestimating the scope of the Flood infection. It is implied that each Halo only kept maybe 2 or 3 spores for study, maybe a few infection forms, and MAYBE some specialized Cold Storage facilities would keep larger intact flood forms (but this is debatable due to the nature of the Halo Array). The Forerunners knew and stated that a single Flood spore could wipe out all life in the galaxy in the Halo:CE Anniversary Terminals (a statement repeated by the Sanghelli in Halo 3 after the Battle of Voi).

So they weren't captured, rather this was probably investigation of quarantined areas turned into desperate attempts to research a magical cure to the Flood, which, according to Primordium, can't exist.

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    Refresh my memory - why can't the cure exist? (link to external page would be fine)
    – The Fallen
    Aug 28, 2012 at 16:38
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    @SSumner, I can't access Halopedia at work but see the article on the Flood or on Halo: Primordium. [SPOILERS]: As it turns out the Flood was made/discovered by the Precursors to spite the Forerunners for not accepting Humanity as the successors to the Precursor Mantle. The flood began infecting humans and humans supposedly found a "cure" in truth the Flood can selectively choose what to infect and what not to infect and that cure didn't exist. Of course, this came from the mouth of a Gravemind, but the Didact seemed convinced though they kept trying regardless.
    – ardent
    Aug 28, 2012 at 16:54
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The Halo installations were primarily designed by the Forerunners as research facilities for studying the Flood. Once a containment breach had taken place, the Forerunners had little recourse but to activate the sterilization protocols in the installations to wipe out all life capable of sustaining the Flood within a substantial radius of the installations themselves.

In short, the Flood weren't captured, so much as they were re-sealed within the installations when the Halos were activated.

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  • IIRC, the Halo arrays were referred to briefly as "Research installations" at some point. My understanding was that some had been stored on the Halos for purpose of research (indeed, if the purpose of the halos was to starve the Flood, wouldn't the Flood have perished in the thousands of years since the activation of the array?). Possibly frozen or placed in some sort of suspended animation - Flood spores, I would assume. If carefully handled by forerunners in suitable protective gear, I would assume that Flood spores could be contained.
    – The Fallen
    Aug 26, 2012 at 18:35
  • Given the rapidity at which the Flood can spread, I think it is possible that when Captain Keyes breached the Flood holding facility, that allowed the rapid growth of the Flood on Installation 04. On Installation 05, there is some speculation that the monitor (2701 Penitent Tangent)'s name has to do with his failure to follow suitable procedures, thus pointing to the cause of the Flood infestation on Delta Halo. Again, the quick spread of the Flood would allow for the rapid overtaking of life on Delta Halo and the Covenant fleet that massed there
    – The Fallen
    Aug 26, 2012 at 18:38
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    @SSumner, The name 2401 Penitent Tangent has less to do with with his failure to follow containment and more with the Forerunners sense of guilt at failing their Mantle-ship of the galaxy. As a result, all Halo installation monitors have carry this motif of sorrow or guilt in their names: 049 Abject Testament, 343 Guilty Spark, and 2401 Penitent Tangent to name the three revealed monitors.
    – ardent
    Aug 28, 2012 at 1:13
  • @ardentsonata - is there an actual source for that? Because I've never seen that anywhere. That seems like another plausible explanation, but unless you have a source I haven't seen - that's all it is
    – The Fallen
    Aug 28, 2012 at 2:56
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    @SSumner, Source for that is the Terminals of Halo: CE Anniversary edition as well as the first two books of the Forerunner Trilogy. In the Terminals, GS asked AT about their lack of access to the Forerunner pool of knowledge known as the Domain, AT responded they didn't deserve to be remembered at all due to the galactic genocide they were to look over. In the books Guilty Spark is created from an early human that was the enemy and then ally of the Didact, Didact's guilt at not listening to the Humans when he had the chance.
    – ardent
    Aug 28, 2012 at 16:34

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