I believe it will be the Culmination of Master Chief's Story along with all other Spartan's in the Books and other Games.
Theory Starts Here:
Master Chief is awakened from Cryo Sleep by Cortana.
She has Identified a Contact with whats left of the ships sensors.
The Ship is recognized as the UNSC Spirit of Fire.
After wandering aimlessly in deep space, they have reached Salvation. Master Chief boards the Ship, alarming a Rampant Serena who awakens the Crew of SoF. Cortana identifies Serena as Rampant and deletes her. Red Team was of the First Awakened from Cryo Sleep and welcomes the Chief.
Since the SoF has no Slip Space Drive (SSD), they send pelicans to recover the Forward Unto Dawn's SSD.
With a New SSD, they jump back to Earth, discovering it to be intact except for the Still Burning Half of Africa.
They contact Lord Hood. They have a Heart Warming reunion. After hearing the MC and Red Team's story, Lord Hood Sends them off in Search of Onyx. Since this is a Top Secret Mission, the newly recovered Spartan Grey Team links up with the UNSC Spirit of Fire and the Frigates UNSC Perseus, UNSC Helena, and the Destroyer UNSC Conan. The 7 Spartans and there Fleet set off for Onyx's last known Coordinates.
They arrive to discover a Massive Installation being Constructed by Strato-Sentinels. Upon completion the Sentinels completely eradicate the Frigate Helena, Using Information Gathered on the Forerunner Language from excavation data on Reach, they present they proper code to the Sentinels and they allow the Ships to pass.
They go through the Portal and Discover it is actually the Dyson Sphere Onyx. The 7 Spartans rescue Dr. Halsey, Mendez, Tom, Lucy, Ash, Olivia, and the others. After emerging from the Portal They discover the Sentinels are under attack from the Flood. UNSC Conan fired it's MAC into a Flood Absorbed Strato Sentinel, bursting it into a thousand pieces. After the Sentinels Mop up the rest of the Flood, The Human Fleet Jumps back to Earth.
Upon arrival, it too is under attack, but this time by the Covenant Loyalists, Spear Headed by Jackals. After fighting a Massive Ground Battle, they receive a Message from the Sangheili pleading for Help. They are under attack from the Jiralhanae. MC, Grey, Red Team, and the others head to Sangheilios to Help.
But this time the SoF was Accompanied by 1 Marathon Class Cruisers, 3 Destroyers, and 5 Frigates. The Spartans are sent to the Ground Battle. The Main attack was centered on the State of Vadam'.
Well, this is all I have so far.
Tell me what you think.