As an avid writer of Halo Fanfiction, I have a few ideas. But I'll just toss one out on the table.
Halo 5: Master Cheif comes to grasp with everything in his life up to this point, From the loss of his friends to the loss of Cortana. All of these things change as he begins to change, since the Librarian accelerated his genetic growth into what she always wanted to happen. He begins to transform into a being to the likeness of the Didact (possibly why he is alone in the E3 video). As the game goes along he becomes quite different from anything we have seen thus far.
Halo 6 (assuming this is the end): Master Cheif has become what the Librarian set in motion on Requiem, he is now all but separate from the human race. He has abilities unfathomable by anyone and he has been connected to the Domain, in which he is connected to a mysterious being that only is a blue light in his subconscious mind. It knows everything about him and shows him what is to come in the near future, a great sacrifice that will either take all life or just one. The game delves into not just Master Cheif but John-117, it tells why the John was the "Lucky One". It also shows how the UNSC is united with the various alien species, and that they live on one anothers planets in peace. But the grand perspective ties back into the "mysterious future" before everything in the universe. John comes face to face with the greatest enemy he has ever faced. The last of the Precursors. He is given a choice to either give up the life on one individual or every living beings life, and the player is allowed to decide the ending to the Halo franchise. This is my brief idea on how it might go, if it was up to me.
