In the year 2552, humans on the planet Madrigal have been fighting 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. After the battle, Master Chief heads to his home planet of Reach with a Madrigal survivor and a mysterious object he discovered on the planet. But a controversial order has John questioning his mission, and himself.

John meets his new partner, and he 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 for her. Makee initiates her plan to retrieve the Madrigal object, with deadly consequences.