The Engineer

"The Engineer" was a fragment of abstracted personality. It was likely destroyed by Flood-infected battleship that had destroyed the Forerunner vessel that was ferrying it to the Ark.

"The Engineer" is the core believed to have maintained Flood life support on many of the Flood's colonies all across the Milky Way Galaxy. It may have contained a comprehensive knowledge of Flood biology, and even their weaknesses.

History
In order to prevent Mendicant Bias from subverting or harming him, Offensive Bias had shattered of Mendicant Bias into its component sections and scattered them throughout the few remaining ships of his fleet for transport to Installation 00, where he would study the fallen AI construct. Much of his fleet was destroyed or ravaged by the Flood. "The Engineer" was most likely destroyed in this manner, yet the Flood may have knowingly have spared it and recovered it. It also may have simply been lost.