So at the end of the game we find out that Director Trench had been corrupted by the Hiss and let them in to the facility using the projector. If this is the case, then why did he lock down the facility? I didn't find any audio record/case file/collectible that would have indicated he was fighting against the influence of the Hiss, and one of his final messages indicates he thinks everyone else has been corrupted by Hedron.
On top of that, why does he shoot himself at the beginning? The cut scene we see where it alternates between Jesse and Dylan sort of implies (?) that the Hiss caused him to do it. It seems like a Hiss controlled director could have furthered their cause a lot easier than a dead one.