Now that I'm going back and playing this classic again, I'm reminded of all the questions I had about the story. I've never read any Halo books or comics or anything like that, so if these questions have been answered in any extracurricular media, I missed it. I tried asking my brother these questions while we played co-op yesterday, but he's no more versed in Halo lore than I am, and tried to spin some fun, silly excuses. I thought I'd ask my questions here.

I gathered that the Forerunners found themselves on the losing side of a war with the flood (side question: where did the flood came from? I imagine maybe the Forerunners made them in an experiment gone awry or something?), so they built a series of giant rings throughout the galaxy that will generate some kind of pulse that eradicates all forms of life everywhere. Cortana says this is so that the flood have nothing left to infect or feed on so they'll eventually die out entirely. Seems clear that the flood had infected nearly all life in the galaxy at this point already, and was so widespread that the whole galaxy needed to be purged, just to be sure they got them all.

Well, why did the Halos need to have an atmosphere, oceans, flora and fauna, and "inclement weather", if they're basically just bombs? Nothing living on the surface of the Halos is supposed to be unaffected by the blast; these weren't supposed to be the last bastions of the Forerunners, were they? If so, what went wrong? (Then again, I'm certain the Forerunners had no intention of surviving the plan; the video from the first terminal I found cemented that idea.)

But then, why were there "samples" of the flood, the very enemy these rings were designed and built to destroy at literally all costs, kept on the ring behind a locked door? Were they too upset by the morality of genocide that they sabotaged their own sacrifice, and the sacrifice of all life in the entire galaxy by preserving the flood for future generations? None of that makes any sense at all.

Finally, why did the original activation of the halos not destroy those samples? I know the sated goal of the halos was to destroy the flood's food supply, and doesn't actually mention killing off the flood itself in any way, but if the flood were able to survive the blast and hibernate for billions of years in a room at point-blank range of the nuke, surely the flood would have been able to do the same throughout the whole galaxy, and would have woken up on their own millions of years ago and infected the dinosaurs.

Looking forward to seeing if you guys can set me straight on these. :) If you've got your own questions, ask them here; I'll probably want to see the answers to those, too.

The floods origins are not known for sure, it is rumoured that they may have been created by the precursors.

The Halo's can only eradicate so much, they can only reach the outer milky way, since the flood cam from further away than that they can't eliminate the flood entirely, not for sure any ways, the idea is that the flood specimens are kept in order to continue researching for a cure if they ever return.

Hopefully I can fill in some blanks here, I know a fair bit about Halo and will try to answer these as best I can.
 
Where did the Flood come from?
Presumably they evolved like any other lifeform in the galaxy. At any rate there doesn't seem to be any evidence for the idea that the Forerunners created them.
 
Why do the Halos have Earth-like environments?
I think the answer to this is that simply, although they were weapons for the Forerunners, they were created to also double up as habitable worlds.
 
Were the Halos meant to be the last bastions for the Forerunners?
No, but they did build worlds that were intended to do that job called Shield Worlds. The Forerunners had every intention of surviving the activations of the Halos, however, they were betrayed by an AI known as 05-032 Mendicant Bias who lowered their line of defence against the Flood and revealed the locations of the Shield Worlds to the Gravemind. All they could do in the end was kill themselves to destroy the Flood.
 
Why were there samples of the Flood?
The Forerunners were doing exactly what we do when encountering a virus, containing it and studying it so they can learn how to kill it.
 
Why did activating the Halos not destroy the Flood?
The Halos don't destroy all life, the Halos destroy all sentient life. The Flood alone (i.e. Without a Gravemind) are not sentient and so were not destroyed by the Halos.

@Gamer_152 said:

Why do the Halos have Earth-like environments?
I think the answer to this is that simply, although they were weapons for the Forerunners, they were created to also double up as habitable worlds.

Were the Halos meant to be the last bastions for the Forerunners?
No, but they did build worlds that were intended to do that job called Shield Worlds. The Forerunners had every intention of surviving the activations of the Halos, however, they were betrayed by an AI known as 05-032 Mendicant Bias who lowered their line of defence against the Flood and revealed the locations of the Shield Worlds to the Gravemind. All they could do in the end was kill themselves to destroy the Flood.

Why were there samples of the Flood?
The Forerunners were doing exactly what we do when encountering a virus, containing it and studying it so they can learn how to kill it.

Why did activating the Halos not destroy the Flood? The Halos don't destroy all life, the Halos destroy all sentient life. The Flood alone (i.e. Without a Gravemind) are not sentient and so were not destroyed by the Halos.

The Halos were created with Earth-like environments to double up as habitable worlds... why? If the Forerunners weren't planning to live on them, who or what was supposed to? No one else in the whole galaxy was supposed to survive once the rings were completed.

Why did the Forerunner AI betray them to the flood? Was his programming corrupted by the Gravemind somehow?

So the samples of Flood tissue kept on the Halo was to figure out how to kill it? But they already knew how by that point, because they built the Halos as a result of that research. There'd be no point in then moving the research lab and its samples onto Halo once Halo was built, because all they need to do at that point is throw the switch.

So the flood can only infect and propagate within sentient life forms? The annihilation pulse from the Halos can somehow filter out non-sentient life? Is there even a definition concrete enough to draw a solid line on that? Regardless, don't we have any evidence that the biomass covering the walls in flood areas isn't created solely through consuming sentient creatures? Hard to imagine they would choose to slam together so many otherwise-useful zombies to remodel the place, especially after the Gravemind was already established.

@Kael: Reclaimers