A SPARTAN II soldier survives the Reach glassing, which run from the planet on a cargo ship he found on the surface...

After a few training missions you discover a Shield World, some sort of "Dyson Sphere" made to protect the Forerrunners from the Halo's blast...

There, sometime ago, the UNSC squad had found a Flood lab, and which they discovered there, they built the SPARTAN-I and first SPARTAN-II's series...

After the defeat of the Covenant, the survivors SPARTAN-II troopers start to behave like the flood... except your, which was the first prototipe of the MJOLINAR project...

Having no other choice, and with Masterchief they enhance our SPARTAN with Human and Elite technology, and with tech of the Forerunners...

Our SPARTAN must find a way to reverse the modifications and eleminate the Flood once and for all...