From Halopedia, the Halo wiki
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 most Flood, including the dead carcasses and destroyed buildings. It can also hurt your troops unless you place them within an airlock.
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 YOU make sure The Flood stays dead, the entire ship will be uncontaminated.