Beginning aboard the Forward Unto Dawn, on which Cortana and Master Chief were stranded after the events of Halo 3, Cortana begins by musing of her seven years of existence and that she has learned a great deal more about the Forerunners than was previously known. The story then shifts to a Forerunner planet before the invasion of the Flood, and then leads up to infection of the planet and it's eventual orbital bombardment.

The Forerunners realize the futility of their actions. They build the Halo network at the Ark and then dispersal them throughout the universe. After the cataloging of all sentient species (of which an early Elite, Brute, Jackal, Grunt, and Human society are shown) The Forerunners activate the Halo rings and wipe out all traces of themselves and the Flood.

An Arbiter named Fal does not want to follow the Covenant religion. One of the Prophets accuses Fal of heresy. Fal will not yield and the Prophet is forced to send another Elite to kill his wife in order to drag him to a trap.

Homecoming focuses on one of Master Chief’s fellow Spartan-IIs as she assists UNSC forces in battle against the Covenant. During the firefight, she experiences a number of flashbacks to when she was a young girl growing up within the top-secret and morally questionable Spartan program.

The story is focused on a marine who is sent to a distant planet to destroy a prototype powered armor. Upon his arrival, he finds the planet is still inhabited by humans who are under the control of the Covenant. With the suit being the only means for survival for the people, the marine disobeys orders and keeps the suit to be used for the good of the people.

"The Babysitter" follows a squad of four Orbital Drop Shock Troopers, or Helljumpers. The squad is composed of Private O'Brien, Dutch, Master Sergeant Cortez, and Corporal Checkman. O'Brien is being replaced as the squad's sniper by Cal-141, a SPARTAN-II, and is now the backup. The squad is sent into a Covenant zone under the cover of a meteor shower to eliminate a Prophet.

On board a cloaked human ship, a group of elite super-soldiers called Spartans (John-117/Master Chief, Frederic-104, Kelly-087, Arthur-079 and Solomon-069) are briefed by an intelligence officer about their mission. A Covenant fleet is momentarily trapped in the system, and is carrying an important "package" the Spartans must retrieve.