Cortana during the end scene in which she fades away touches the Master Chief physically. This could mean without her knowing (due to rampancy on her knowledge data banks) is stored into the Chiefs Suit. By doing this it would take her time to regrain her strengh inside the chief and unable to notify him. Which on that note would make a great game scene about the master chief on his knees in mortal peril and an enemy boasting "You are all alone, Your death is at my hand" or some other boastful line where Cortana (Who has regained her strengh) say's to the chief "GET UP JOHN". The death of Cortana effects him hard, effecting his combat ability. With the resurgence of Cortana the Chief gets back into action.
