Interesting thoughts. Have you seen the promo for the new episode yet? It has me thinking about the fact that the Machine has been communicating with Root in a way we haven't seen it (or her) communicate with anyone else before. With Finch, it responded to what he taught it and answered his questions when he was teaching it and it gives the numbers to him and to the relevant side. And it created Ernest Thornhill and hired people and rented cars and an office etc. And has been trying to convince Root to not murder her doctor. And then there's the promo...

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In the promo... a guy gets into an elevator and a very disembodied, computer-like voice says something like "you've hurt a lot of people" and the elevator starts falling fast. Could this be the Machine taking matters into its own hands to stop a number that's a perpetrator?