Master Chief is not in Halo Wars. However, there are three main Spartan IIs in Halo Wars and Spartan IIs who are unnamed that you can train for your army.
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Master Chief is a Master Chief in the UNSC (A fictional branch of the military) and is the highest enlisted rank attainable.
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Cortana is the name of the Master Chief's AI side-kick.
The Master Chief is actually a Sangheili Councilor who wears a MJOLNIR amour suit.
The Halo Series