User blog comment:James12708/Bioware Hasn't written themselves into a corner/@comment-2250460-20121109160659/@comment-2250460-20121109172333

She is warning you of the Didact and more Forerunners, it is no secret who she is referring to.

As for the Flood, they have already been defeated. The only other possible thing she could be referring to, and it's a very slim chance, are the Precursors.