Interesting Spoilers
Here's some spoilers which I felt needed to be posted in spoiler theories. This is due to the fact that I'm incapable of providing 3rd party corroboration with a reliable source, so I'll keep these here until they pan out after season 3
- We'll find out that "Ben Linus", along with Richard Alpert and Jacob, were once workers for DHARMA who also doubled as human test subjects for various DHARMA projects on the island.
- We'll see the overthrow of DHARMA scientists by the workers led by Jacob, who was the instigator of the revolution and the saviour of Ben. Unfortunately, Jacob was unable to save Ben's family which we'll see.
- We'll come to understand that the mysterious (this name is a spoiler until it is told to us in an ep) wasn't the only traveler on the expedition flight to the island (hint: a male was with her who'll wash ashore later), but is in fact a spy of the DHARMA Initiative who's come to investigate exactly what happened on the island.
- The triggers for her visit were the meltdown of the Swan Station and the loss of contact with the Flame Station. A series of "secure" codes had to be input from the Flame to give DHARMA the green light that everything was fine, and to continue the food drops the same way the numbers had to be input in the Swan. The Others (hostiles) were successful keeping up appearances with Mikhail's help until Locke destroyed it.
- Cerberus, aka "The Smoke Monster" was a DHARMA experiment in both nanotechnology and neural networking which was used to guard the perimeter of various stations intuitively, but was damaged during the purge of DHARMA controllers, It has since gone rogue and become self aware.
- The "Others" as we've come to know and love (or hate) are truly the good guys who gained their own freedom and were actively attempting to reverse the effects of experiments performed on them by DHARMA, and the effects of the island on unprotected humans until Flight 815 interrupted them.
- Ben confides in Locke that they were basically slaves to DHARMA and they must keep up the ruse that DHARMA is still in control or they will all die from a common enemy. Jacob is the head "inmate" who orchestrated the revolution, and who remains hidden in plain sight but is still the one they must answer to.
- We find out that Penelope Widmore has been a member of DHARMA all along, and the station in Antarctica is run by DHARMA. Desmond has a vision of Penelope which is frightening and reveals new, truthful memories about how they really met at the monastery
- Ben dies in the finale along with a few Others, as does Kate and Sayid. Sawyer and most of the Losties blame Jack and Juliet for Kate and Sayid's deaths due to his plan. Jack is forced to go with the surviving Others, and we see Tom by his side as he protects his new leader. From the sky we see images of the island as if from the viewpoint of a coming aircraft. It seems DHARMA has sent someone (or something) to the island and it's not nice.
Source: The Fuselage
