The New enemy in halo 4 has a very very good possibility of the enemy being timeless one and how he can control the flood since the precurcers created the flood as a last resort encase the forerunners won the war if you can find the video on youtube of all the concept art put together it looks like a precurser and you can see the 2 legs in back and in front the ugly face how huge his body is and the precursers giant oval eyes the timeless one was inprisioned by the forerunners after a huge forerunner precurser battle 150,000 years before the events of halo ce he escaped after the prison was destroyed and since humans are basicly the forerunners timeless one wants to destroy the human race and engulf the galaxy timless one and his people created the forerunners and the flood the forerunners turned against them or didnt have the same thoughts on things and wiped out every precurser in the universe except 1 which has livid for a very very long time and probably know how to control the flood
so my theory is that you battle the flood and timeless one and possibly some forerunner technoligy he knows how to control and later the covenant and humans find the cheifs signal/beacon and come help after he crashes on the planet and explores the new weapons enemys and enviroment