Honestly, I'm puzzled. The first scene with Arbiter interrogating Chief was at night, and the last scene with Arbiter at the window was at day. I doubt the toys fought for that long though. The gunshots puzzle me too.
One idea is that maybe Eugene didn't shoot himself, he just shot the wall or something, and he tracked them down. Eugene probably shot Jon outside and blamed him for what the toys did. If Eugene went into the apartment, he'd be terrified to find out they are alive. If Eugene twisted Chief apart or something, why wouldn't he do the same to Arbiter? Why would Aribter wait that long to kill himself?
Maybe one of Eugene's "faceless army" did it.
Maybe Arbiter twisted Chief apart in a fit of rage.
The blood could have been caused by Greg. Greg is a real spider. I doubt Jon had a gun in the apartment though, because Chief would have done something stupid with it by now.
My thoughts on what may happen:
What do you think?