I have been listening to the sound that is made when there is a transition between the island and the flashes back to whatever timeline and I swear the TARDIS engines when materializing is part of it. I have gone back and forth numerous times this morning and this seems to be the case. I was re-watching the Face of Evil and during the beginning of the episode when the TARDIS makes its first appearance there is a rather long materialization process and that is part of the sound used on Lost. I not asking anyone to take my word for it just go check it out for yourself.
Also I noticed that there is a banishment scene at the beginning of the episode that is reminiscent of Widmore being exiled off the island.
Reply: The Doctor when he first arrives breaking the fourth wall he tell the viewer that “There seems to be a nexial discontinuity.” To me this would suggest that this is a nexus point and the place is ripe for bringing about change to the universe without causing a paradox and thus an alternate reality.
When he first meets Leela she calls his the “Evil One.” He then offers her a jelly baby (candy, the Doctor’s favorite treat) and she replies with “It is true they say the Evil One eats babies.” He then tells her that she should believe everything she hears. This scene was reminiscent of the conversation with Widmore and Flocke when Widmore described his knowledge of Smokey via myth – ghost stories and jungle noises in the night.
Reply: In the Face of Evil Story the Sevateem believe that the Tesh have imprisoned their god Xoanan. They are planning to attack the Tesh in order to free him. It would be ironic that if in the story of Lost if Jacob the one who they believe is good actually imprisoned the MIB who they believe is bad almost like this story.
Reply: It does and I agree with you on that point also. Again I can't explain a sound to you and I know what Charlie meant when he said I have to show you. If you viewed a copy of the Face of Evil (It's out there on the internet you just have to find it) you could hear what I'm talking about.
Reply: There was a part in The Face of Evil where Neeva (the spiritual leader of the Sevateem) was praying to Xoanan for guidance on the attack that they were about to carry out on the Tesh. I equate Neeva to Richard as Jacob has actually spoken to him. Just like in the Face of Evil Neeva hears Xoanan’s instructions over the communications device in the space helmet that he dawns as a religious artifact. The Doctor and Leela were at the rear of his hut listening. Another tribe member came to get Neeva as they were ready to proceed with the attack.
After Neeva exists the Doctor and Leela have the following conversation:
Doctor: You know I had a feeling, (short pause) I had a feeling that Neeva was actually expecting to hear an answer to his prayer
Leela: There wouldn’t be much point in praying if he didn’t
Doctor: I can quote you a few theologians who would give you an argument on that.
If bring this point up because the reason that the Doctor gets into Xoanan’s temple is that he used/tricked Neeva at a later point in the story to answer a question of where else he had heard Xoanan’s voice. Xoanan’s voice and the Doctors are the same. Neeva responded that he only heard it in his hut. The Doctor deduced from that there had to be a way to cross the impenetrable time barrier that had been setup to reach the Tesh side of things since a radio wave could get through. Essentially the Doctor used a loophole as you might say to enter into Xoanan’s temple in order to repair him (essentially killing off his personality from that of the Xoanan entity to make it sane again).
To me Richard was used for the same purpose. He was tricked by Flocke to get Ben into Jacobs’s temple for the purpose of Ben killing Jacob. They were both used as pawns to bring about the destruction of Xoanan and Jacob. Since Xoanan was only repaired that’s why I like to think of Jacob as not gone but in need of repair.
Note: Richard as far as we know is the only one who knows for certain that Jacob is truly real because he has seen and heard him. Neeva knows that Xoanan is real because he hears him all the time and gives him instructions to give to the rest of the Sevateem tribe. Almost like the slips of paper that Ben spoke of receiving from Richard concerning Jacobs’s wishes. “All those lists.”