Master cheif will meet the Arbiter, and the Ark will reveal to all that humans were the Forerunners, so with the UNSC out of the way, the Arbiter returns and takes command of Johns military, as they destroy the real heretics, The Prophets. In the end John is made king of a Second foreruner empire.
At the end of the game after the credits it will flash to 10,000 years later, a scientist is working on a eirily familiar life form,GASP! the Flood!!! Pan to the palace on earth, an alarm goes out as infected vessels slam into the planet, all the rings are activated, but in a small shelter we see a small boy with mixed species of survivors, and he looks quite similar, the end.
Disclaimer: I do not work for Bungie, or have friends that do all information provided is speculation, and speculation only, any similarity to the planned ending is purely coincidental, and unintentional.
Shovels down, Shovels up this trench better hold up as " Skull Legion" goes fighting along.
Our Motto: When in Rome do as the Legion does, kill, ravage, destroy; anything to make those Covenant SOB's forever sorry of the day they met the human race.