From Halopedia, the Halo wiki
This is a short mission if you want it to be short. Start by constructing turrets near the airlocks and upgrading them to anti-infantry turrets, place your spartans here to help protect the airlocks. 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. Air troops cannot be placed in an airlock but they can be moved in the direction opposite to the shield's advance to minimize damage. Turrets also take damage so they should be healed or replaced when their health gets too low.
If the flood buildings still haven't been destroyed by the third wave of the shield, then two Vultures will come down to assist.
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.