I think he's freaking out because they are like glitching out. Normally when Mr Robot takes control Elliot is completely unaware. Now there are times when he can see Mr Robot in control. Some theories I read is there could be another "operating system" breaking through, so there is a third Elliot we haven't seen yet. That's just a theory though on why he's glitching out.
Has anyone seen the zoomed in frame by frame of the final scene? Looks like Cisco got blasted and Darlene probably didn't get shot or if she did in the arm
I don't think the Dark Army would want to kill Mr Robots sister, shoot some think Mr Robot may even be leading the Dark Army. We know at least Phase 2 is his plan and they are going ahead with that plan.