In the year 2552, humans on the planet Madrigal fight for independence from Earth, but a fatal encounter with the Alien Covenant complicates things; Master Chief John 117 and his super-soldier "Spartans" join the fight.

John takes Kwan to an old friend and learns more about the mystery object, which the Covenant and Makee are determined to steal. With the alien threat growing, Dr. Halsey has a plan to deal with John's unpredictable behavior.

John meets his new partner and discovers secrets in his own memory; Kwan wants to continue her people's fight for independence, but Soren has different plans for her; Makee's plan to retrieve the Madrigal object has deadly consequences.

Guided by his visions, John takes Halsey and Cortana back to where it all began, looking for answers from his past. With Soren along for protection, Kwan goes in search of an army.

On the run and out of options, Kwan and Soren have a difference of opinion. With the possibility of finding the mysterious Halo on everyone's minds, John makes a horrible discovery. And the war rears its ugly head.

Survivors of the battle with the Covenant return to Reach. John confronts Dr. Halsey and her lies. The new prisoner seems to know John better than he knows himself. The mysterious artifact shows John something startling.

John and Makee come to terms with their shared vision. Halsey has one last chance to save her mission, and herself. As things come to a head, everyone must choose a side.

Beaten, battered, and betrayed, John 117 leads the Spartans on a suicide mission to find the Halo and save humanity.