Here's what I think is going to play out here. We've ruled out options that High Charity made it there on it's own, or that it used brute force through slipspace shenanigans to enter the pathway that the portal led to. So, that only leaves expanding the portal to accomodate for the station. And that means that the ship has to enter the atmosphere to do so. Now, 343 already did some expansion on what happened to Africa during the first wave of Flood forms. Cities were overtaken in hours. So, to make things seem even worse, and to make the Flood more of a credible threat, High Charity does launch more flood out and about. Now, how does basically a small resistance force of Human military stand up to this? We've got two options. 1. Scorched Earth policy. There was still several Mac platforms orbiting Earth even after all this shit plowed through everything. The flood pods are tracked, and wherever they land, the UNSC opened fire with the orbital platforms with everything they had until there was nothing but craters and dust. This is, probably unlikely. I don't have the math for the yields that a MAC slug does, but I know it does a hell of a lot of damage. And firing that into the atmosphere multiple times would cause a metric -blam!- ton of damage to the planet. However, it would add another element to how desperate things were. If the Flood landed in cities, the UNSC fired for the greater good. 2. The UNSC gets outside help. Where from? More Elites/Covenant seperatists. The schism split everything apart, and during this period, there was probably hundreds of self contained skirmishes all over the place between Covie loyalists and seperatists. The battle at the Ark was a big one, but I'd be willing to bet that it was only one small part of a larger picture. These Elites show up late for the party because they've been busy doing other battles elsewhere, but heard Rtas's and Thel's rallying war cry. They show up in the nick of time, and help the UNSC glass and contain the Flood while High Charity has already pissed off on it's merry way to the Ark. This would help seal up the boo boo about High Charity getting to the Ark, make the Flood out to be more of a credible threat and danger, and possibly open up more pathways to more friendly Elites that we could see in the future. Hell, for fun, they could even make some Spartan Assault missions based around this. Don't that all sound fun?