I think this is what it is all about. An ultimate twist, a cruel fate.
The Forerunners created the Flood and used it against the Precursors, wiping them out.
The Flood then evolved and turned on them.
Short, sweet, and to the point.
This is the act of barbarity described in Silentium.
Discuss.
[Edited on 08.29.2012 11:34 PM PDT]
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I don't think your theory is entirely spot-on, considering that the Flood originated from outside the galaxy and the Forerunners, being a Tier 1 civilization, did not possess the capabilities of intergalactic travel.