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I wondered how Daniel Faraday learned about the DHARMA Initiative when his mind was so messed up. Based on last night's episode, I think alot of the notes in his notebook come from his flash sideways self. Some of the stuff he is writing in the original timeline is also appearing in his FST notebook.
Here are some other times where the characters may have been experiencing visions from other timelines while Slipping in and out of concsiousness.
Theresa: Speaking with her father who died 5yrs ago Juliet: Telling Sawyer "It worked" Charlotte: I'm not allowed to have chocolate before dinner Charlotte: "Look for the well, you'll find it at the well" Minkowski Desmond: Seeing Claire and Aaron get on a helicopter.
As for their minds flashing betweem timelines, I think Desmond has swapped. The FST Desmond is now in the OT. This is why he is so willing to help Widmore because he is his right hand man in the FST. OT Desmond is now in the FST and wants to recruit the 815ers in order to show them they are in a wrong timeline and that they need to course correct.
Widmore did tell Desmond when this is over, I am going to ask you to make a sacrifice. Chances are FST-Widmore will ask OT Desmond to sacrifice his relationship with Penny
Eloise. I'm still confused. In the FST, she knows who Desmond is for some reason. Has she been flashing back and forth too?