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Originally Posted by
videobruce 
This seems to be turning into a 'Fringe/X Files' series. I kinda got lost over the past couple months.
They couldn't just keep doing the number thing all by itself. Yeah, the numbers are at the heart of the show, but you run out of interesting subjects. So they have broadened it into Reese's past with the CIA and how he can never completely get away from it, which is what he had been trying to do when the show started, Carter interrogated him in the pilot when he was dressed as a homeless person. He is now on more radars because of the good work he is doing. The exchange between Fusco, the HR informant, and Reese about you never get your hands clean extends to Reese as well. His hands are very dirty and he is trying to get them clean by helping those who can't help themselves but it ain't easy. Then there is Finch. Is his hands dirty? Did he have anything to do with "The Founder" of the machine's death? Ah, the questions. The questions.
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The nice looking CIA (?) chick, exactly who is/was she?
That is the "person of interest" (pun intended) we are not sure if is alive or dead. The CIA guy keeps saying Reese killed her, but Reese is thinking of her in these flash backs when he first joined the CIA. Some think she may be the hacker from several episodes back that crashed Finch's computer systems at the abandoned library. At this point, there is not enough back story out yet to determine what happened to her. At this point in the storyline, I would hazard a guess that the hacker IS her. She certainly exhibits the smarts to do something like that in the flashbacks. But then there is Eliza still out there. He too could be mixed up in this somehow.
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That CIA guy who just got kidnapped, what's the deal with him?
It would seem he had gone rogue and is considered to be in the same class as Reese as far as the CIA is concerned. I think the CIA "bagged and tagged" him, so to speak. I think they killed him for going outside of "the company" to do the drug deal and then it went down way too messy.
Lots of loose ends here. Your guess is as good as anyone else.