I've had this in the drafts folder for a little while. I thought I'd finish it out, clean it up, and post it.So, I've been playing through some Halo 3 campaign levels recently, (Matt and I have been helping eachother get the scoring achievements) and I realized something about the end of the game.
Warning: What follows is a far too in-depth analysis of nit-picky details in the story of a video game about shooting things. If you haven't played the Halo series, I can pretty much guarantee you won't care. Also, spoilers! Oh noes!
By firing Installation 04 2.0, our heroes basically ruined their long-term prospects. Yes, they destroyed the entire contingent of Flood on the Ark, and with it the Gravemind (regardless of whether or not you accept that the Halos kill Flood themselves, since Gravemind is a sentient being, it falls under the umbrella of the Halo network's ambiguous killamajig). But, if Installations 04 and 05 are any indication, there is a high probability of Humanity (or somebody else) encountering a serious infestation of Flood at some point in the future. Sure, it's all well and good if you can effectively quarantine them on the ring; Master Chief was able to do that with Installation 04. But in Halo 3, we see what happens when a coordinated Flood infestation gets off the ring: mainly, everybody's screwed.
In the course of what can't be more than a couple of days (from the time Regret's fleet arrives at Installation 05 to the end of Halo 2) the Flood manages to assimilate a large combat force, expand its control outside of the ring's quarantine zone, and establish a foothold on its most powerful adversary's most significant vessel. In what can't be more than a couple of weeks, (between the time Truth's fleet leaves High Charity for Earth and the events of Halo 3) the Flood has managed to break the Covenant's quarantine efforts at Installation 05 with at least one infected ship and make a charge for Earth. This is soon followed by High Charity itself, now completely infected, and serving as a mobile base of operations for the Gravemind. While these two threats are contained, with the Shadow of Intent glassing east Africa and the firing of Installation 04 2.0 respectively, it is reasonable to believe that there are other infected ships somewhere in the galaxy. Despite their reliance on the tactic of overwhelming force, it would represent a significant strategic blunder for the Flood to send its entire strength through the Ark portal.
This is the important part. Even if one accepts that the entire active contingent of the Flood followed Covenant, Humans, and Elites to the Ark, and were eliminated by the firing of 04 2.0, there are surely more dormant populations on the other five Halo installations and research facilities like those on the Threshold gas mine as seen in Halo 2, if not more active populations like that encountered on Installation 05. So far, the only successful methods we've seen for wiping out an infestation are the complete destruction of the infested area (as in the case with Installation 04, the Threshold gas mine, and East Africa) and the firing of the Halo network (as was the case in the Flood/Forerunner war). Therefore, to get rid of the Flood means to either destroy the Halos and all related facilities in the galaxy (which, considering the reach of the Forerunners, represents a daunting, if not impossible task), or fire the Halo network once again.
With the Ark presumably destroyed in the premature firing of 04 2.0, there is no way to fire them safely, without wiping out the vast majority of sentient life in the galaxy. If there is a Halo 4 as is rumored, it will be interesting to see how Bungie handles another appearance of the Flood, story-wise. It seems to me that they should leave things where they are, lest they be forced to invent something ridiculous to explain themselves.
