: Some Forerunners survived at the Ark, but back then there wasn't a Halo fired
: point blank above it. All of the Halos were down in the galaxy and the Ark
: was outside their range.

The Ark no doubt held a repository of genetic material for the re-seeing process. My first reaction was that the Ark's systems must have started malfunctioning, thinking it was time to re-seed the galaxy again, and just started producing every sort of creature held in its banks. That would mean, despite being the target of a Halo blast, it's habitable zones would now be chock full of deadly creatures, all competing for survival.