The ninth season starts out with two independent plots – one in machinima style using the Halo: Reach engine, following Church after he transferred himself into the capture unit following the finale of season 8, and another, an entirely CGI-rendered storyline chronologically preceding the Blood Gulch Chronicles, involving earlier events under Project Freelancer.

In the capture unit Church attempts to straighten things out with the members of Red Team, as he discovers they aren't behaving the way he remembers them to. And after coming back from being shot in the foot, Church finds out that Caboose called command, and tries to find out which Freelancer is coming, in high hopes that it is Tex. In a flashback of Project Freelancer, twin operatives North and South Dakota steal a data file from a cryogenics facility. They are found out by the facility guards, but are soon rescued by another Freelancer, codenamed Carolina.