I think we’ve all thought of this, what might be a plot hole in Halo 3. When High Charity arrives on the Ark, it had to have gone through the Portal on Earth. Now Gravemind, must have sent some Flood forms to the humans. Now, why when we see the ending before the credits, is there no Flood? Unless the Sangheili helped exterminate the infestation, how could of we have stopped the Flood? Maybe no Flood forms were dropped down, seeing as Cortana did say, that “High Charity’s on its way to Earth, with an army of Flood.” Which would seem odd. What do you think?
Hmm, very interesting. I never thought about the idea that High Charity would have to enter the portal to the Ark that’s located at Earth. It would be really stupid if The Flood wouldn’t attack Earth with a few drop pods while they were there anyway.
Maybe Earth fought them off? I mean, they were prepared for it, seeing how Lord Hood stayed behind to prepare for Earth’s final stand against The Flood.
Video
Also, this video says Lord Hood prepared to fight The Flood, but Master Chief stopped The Flood from coming. If you would have to believe this video, The Flood never passed Earth and must have found another way to the Ark (which seems highly unlikely to me 
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It is strange but the only explanations we have are:
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It jumped there. But this may of taken too long.
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It arrived at Earth and went straight through the portal.
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Or it was fought off by the Humans ate Earth.
I think 2 is the most logical but we may never know.
the flood stopped when gravemind retreated and masterchief blew up the halo