“Power Hungry” confirmed my speculation regarding how the very dead John Scott was very much alive in Olivia’s head – the synaptic transfer that the pair went through in the pilot episode left a permanent imprint on Olivia’s mind, giving him access to her consciousness and presumably allowing her access to his.
But this is Fringe and very rarely is anything without a further twist. Two key scenes at the end of the “Pilot” and “The Ghost Network” serve as a massive reminder of the larger players at work – Nina Sharp and her Massive Dynamic corporation have John Scott’s dead body and they’ve been doing things with his mind. Assuming that the encryption key, given to Nina by Phillip Broyles, has given them access and perhaps control over John Scott’s mind (a part of which now resides in Olivia’s), could it be that the John Scott that has been interacting with Olivia is nothing more than a ‘puppet’ being operated from afar by Nina Sharp in order to manipulate her? Did Nina sabotage her speculated ‘business associate’, Jacob Fischer, by using ‘John Scott’ to help assist Olivia in his capture, in order to find out how and why Olivia is so connected to “The Pattern”?
With the second coming of Agent Scott possibly being directed and controlled by Nina Sharp, can Olivia ever really trust him again?