Cleansing/Walkthrough
From Halopedia, the Halo wiki
Overview
This is a short mission if you want it to be short. Create a ton of Hornets and start destroying The Flood on the rear of the vessel.
The ship will soon fly through a big energy field which disposes of The Flood, especially the dead carcasses and destroyed buildings. It also hurts your troops.
The 11th Black Box can be found by a Hornet; Search the left side of the rear, as it's on a wing. The Skull in this level can be found after killing 100 Sentinels and then securing it by sending a Hornet to explore the front deck of the ship.
When the shield has passed over several times - while the only thing that YOU need to do is making sure The Flood stays dead - the entire ship will be clean.