Mendicant Bias was a Contender class Forerunner AI. The most powerful of his kind. Why was he so powerful, you ask? Well, the answer is simple. MB had the powers of a normal AI, PLUS the mind of a living being. Which living being? The Didact? The Master Builder?
No. The Precursor Prisoner.
Why didn't the Forerunners just kill this beast on sight? Because they wanted to use it in an AI. The Precursor made the Flood(probably), so this guy should know all about it, right? And so, they did. If you read Contact Harvest, you know the part where Sif is talking about combing her hair. Each AI retains something from its maker's memory. My guess is that MB retained the part of the Prisoner's mind about killing all Forerunners. Thus, he allied with the Flood and attempted to kill the Forerunners.