In my story, Mendicant Bias lives his early life as an AI who becomes corrupted by the Primordial. Eventually, Mendicant Bias destroys the Capital World and leads Flood attacks on Shield Installations, such as Shield 801. He devises a plan to destroy the last Forerunner bastions. 4.8 million warships attack the Maginot Line. This is a distraction for the Forerunners at the Greater Ark and allows Mendicant the element of surprise. Eventually, his forces badly damage the Greater Ark. Offensive Bias arrives and stops Mendicant. Offensive places Mendicant in dormancy but learns this is only a fragment. The real Mendicant returned to the Maginot Line. Eventually, Mendicant is defeated at the Maginot Line.
Once the Halos are activated, Mendicant is returned to the Lesser Ark for judgement. One of Mendicant's splinter fragments escapes on a Keyship. Eventually, this Keyship finds its way to the San 'Shyuum. We all know that story. The real mendicant is stored on the Ark for all eternity until he is reunited with the splinter fragment.
As for the Fragment on the Greater Ark, it forces itself out of dormancy and waits, thinking back. Thinking again about Atonement. This fragment is forced into dormancy again by the Overseer, who escaped the destruction of Installation 01. He will be reawakened by the UNSC years later. They would use him to combat the Second Flood Outbreak.