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 behaviour.

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

John takes Halsey and Cortana to look for answers from his past; Kwan searches for an army; John's behaviour inspires another Spartan to begin a journey of self-discovery; Miranda discovers a possible link between the artefact and something larger.

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; the war rears its ugly head.

John confronts Dr. Halsey and the lies of his past; the new prisoner seems to know John better than he knows himself; determined to understand more, John turns back to the mystery artefact, which shows him something truly startling.