Board Thread:General Discussion/@comment-99.114.158.21-20131111024513/@comment-2045210-20150816083755

Perhaps the Director wasn't exactly trying to "protect" the Alpha but to hide it and sent Flowers to protect it. (That contradiction)

As for the simulation thing. Maybe they didn't really follow a "strict script" but dumped the sim troopers into a freeroam area where a bunch of events were thrown at them that were planned out by Project Freelancer.