I have thought alot about the end of halo recently and this is what I have come up with. 

After the Master cheif has survived every faction imaginable, blue team has died (Not stupid reach deaths, but heart felt meaningfull deaths), Halsey and Lasky have been killed, and the Infinity has crashed putting mankind back into the previbial stone age the MC finally makes a one cyborg assault on the Didact on the recently rebuilt Requim.  

Half the campaign would be in Requim and the last level would just be a boss fight with the Didact.  After the long battle the didact is exhausted and badly injured.  He asks John "Why are you doing this for humanity?"

And then John simply replies "I am not, I am doing this for Her."  He makes the cu de grace and leaves.