The chief totally read as suspicious of Abby for generic cop reasons to me. I don't think it's what's happening here, but that would be a brilliant idea for this setting, for a villain to manipulate the hero to cover things up or give them a rational explanation by appearing totally focused on paperwork or prosecutable cases or whatever.

I guess we'll have to wait and see what other characters wander through and where they go with it, but even with Cho and the secret investigation, the pilot seemed to me to be much more straight up battle between good and evil than tricky shadow conspiracy.