So halo 3 wrapped up with a nice little ending with the covenant alliance falling apart, truth was silenced, and the flood threat was eliminated... right?
I say wrong.
And here is my evidence
"Knowing that it faced its own complete extinction, what remained of the uninfected, stable specimens fled the galaxy aboard a commandeered vessel, destination unknown and remained dormant for thousands of years, biding it's time."
http://halo.wikia.com/wiki/Flood
As we all know, the flood are ruthless. The scary thing about the flood is not necessarily their combat abilities... a single combat form alone really stands no threat against an agile warrior. But what about 7 billion? Thats when things get a bit scary.
The flood retreated to 'god knows where' for literally thousands of years. Who knows what planets they came across, what civilazations they conquered and the sheer mass that they eventually required. When you really start to look at the cosmos as a whole, an infection like the flood NEEDS to be stopped early. And the flood was not.
So i say that no matter what happy ending halo shows or bungie or 343 wraps up with, eventually more flood will come... and they will suceed.