User blog comment:Prometheus5/The Flood vs Skynet/@comment-108.238.89.32-20151218221646

The Flood wins because Gravemind Flood forms can server AI's and no matter how "intelligent" Skynet is, Skynet is still and AI.

"Gravemind is able to subvert AIs. In the Forerunner-Flood war it was capable of altering every Forerunner AI's basic logical processes, causing it to aid the Flood cause. This 'Logic-Virus' was considered by the Forerunners to be the informational form of the Flood infection, to which Mendicant Bias was the first victim in its 43-year discourse with the Precursor Gravemind."

http://halo.wikia.com/wiki/Gravemind