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After 28 years of drifting in space the UNSC Spirit of Fire finds it's way to the orbit of the Forerunner Installation 00, known as the Ark. Awakened from the cryo-sleep, crew eventually travels down to the Ark to find out how to establish a contact with the galaxy. However on the surface of the Ark they encountered a hostile, violent mercenary faction known as The Banished, led by the cunning Jiralhanae warlord Atriox.^[1]
A Sangheili shipmaster returns to the glassed human colony of Kholo^[2]. The species wide war between the Sangheili and the Jiralhanae is still ongoing^[3] .

Sources

^ GameSpot: Halo Wars 2 New Story Details and Images Revealed
^ Halo: Evolutions - Essential Tales of the Halo Universe, "The Return", page 492
^ Halo: Evolutions - Essential Tales of the Halo Universe "The Return" - "It was a terrible war. The Prophets provided the Brutes with powerful new weapons, hoping that they would in turn defend their Prophets against our wrath. But when the Prophets went into hiding, the lack of leadership allowed the Brutes to return to their savage nature and they soon began to fight against each other. This lack of solidarity made them much easier prey. Some of my fellow commanders continue that fight even now"