Through the Looking Glass by EmilyG

Someone is coming to the Island, Jacob tells Hurley. They're coming, Jacob tells the MIB. Here's my (incredibly convoluted) theory:

1) THE ALT IS COMING: Specifically, the Dharma Initiative from the ALT reality is coming to the Island. "Over There", most of Dharma's personnel were evacuated immediately prior to the Incident, and those that were left managed to escape before the Island sank (a la Ben).

Decades passed, and Dharma was unable to find the Island (as it was lying beneath the ocean). Until something happened: there are many possibilities---Flight 815's arrival at LAX, Jacob's death on the Island in our timeline, the arrival of the Losties in 2007 of our timeline, or a number of other things---but something happened which made the Island "visible". Dharma could "see it" (via their instruments) but they couldn't reach it---all they physically 'saw' was empty ocean. That is, until Jack smashed the mirrors in the Lighthouse: smashing the mirrors = smashing the barrier between the two worlds (as it seems very possible that the mirrors were showing the ALT, not "our" Losties' childhoods). Dharma can now come to the Island.

2) THROUGH THE LOOKING GLASS: Dharma thought Sayid was raving in 1977. He spoke of Flight 815 crashing, Ajira 316 landing, and DHarma being wiped out---three things that never happened in the ALT. So Dharma arrives, all ready to go mano a mano with the Hostiles---only to encounter a few very strange things. The fuselage of Flight 815, which they know for a fact LANDED IN LOS ANGELES, is sitting on the beach. There are a bunch of dazed survivors of flight 316, which NEVER WENT MISSING, wandering around Hydra Island, saying something about a man who insisted he was dead, a missing pilot, etc. There's a pit filled with long-dead corpses wearing Dharma's clothes. They find videos in several of their hatches dated AFTER they left the Island, detailing experiments they never had a chance to complete. And now that they've arrived, they can't make contact with the mainland. Oh, the mindfuckery.

And who makes up the new Dharma Initiative? Older Horace, older Radzinsky, older Amy, I'm sure. People who will be haunted by "visions" of their lost and betrayed friends---LaFleur, Miles, Jin, etc---constantly seeing their "dead" friends in the jungle, seemingly unchanged. Oh, the mindfuckery.

But say, for example, they recruit one Dr. Juliet Shepherd, ex-wife of Dr. Jack Shepherd. ("Wow", they say, "You look just like "her"", thinking it's a giant coincidence that this Juliet looks just like the 1970s Juliet.) Sometime between the flash-sideways of "Lighthouse" and Dharma's arrival in 2007, ALT Jack dies. David had just begun repairing his relationship with his dad, and he's heartbroken: Juliet, David's mother (and oh, how I hope she really is the mom) brings him with her to the Island in order to break him out of his depression. But she starts to "change" on the Island, becomes more assertive, more kickass, the longer she's on the Island. She feels drawn to the jungle, feels like she's been here before.

And then David starts seeing his dead father walking around in the jungle.

Maybe Alt Claire is recruited by Dharma. She brings her toddler Aaron---only to have one of the Hostiles be desperate to kidnap her son. After weeks of this, she comes face-to-face with the attempted kidnapper: herself. Oh, the mindfuckery. Dharma recruits Charlotte Lewis, anthropologist extraordinare, to study the "hostile indigenous population". Etc., etc., etc.

Dharma is now "the newcomers" and the Losties have now been subsumed into the Others. The MIB takes control of the Others, as the Losties won't leave without "their" people (those who died in the original timeline, but have now traveled from the ALT and are living in the Barracks). Lists are drawn up, and those people---those the Losties knew in the past---are kidnapped from Dharma's camp. It's season 1 all over again, but roles are reversed: now the Losties are the mysterious figures in the jungle, and we actually know the reasoning behind their insane actions.

3) WIDMORE'S LONG CON: I think Widmore's been doing the same thing Sawyer did in Season 5---playing a long con against Dharma in order to put himself in a position of authority within Dharma so that he can rescue the people on the Island.

When Alt Dharma initially arrives, they try to release the gas at the Tempest to wipe out the Hostiles, who have conveniently gathered in a central location, the Temple. (This is why Jacob wanted the Losties to leave the Temple---it's like shooting fish in a barrel.) But the gas has already been turned off by Charlotte and Daniel, operating (I think secretly) on Widmore's orders.

Hostilities begin.

Dharma knows it needs to get rid of the Hostiles' leaders---the survivors of Flight 815. Dharma is probably going to figure out how to manipulate the Island's energies to time travel (on an individual basis)---but they'll be doing it within "our" timeline, not their own. I think we've been seeing this throughout the last five years. Sometime in the past, Widmore is warned by a time-traveling Desmond about the coming danger. He then works to build up his power, wealth, and prestige in the outside world; upon his exile, he is able to present himself to Dharma operatives (originally from the ALT, now time-traveling into "our" timeline's past) as a wealthy financier with no ties to the Hostiles or the Island. His background must be documented, must be unshakeable, because Dharma is understandably afraid of infiltration by their enemies.

From Dharma's POV, Flight 815 cannot crash on the Island, or Dharma will lose the war. Dharma operatives get the pilot of the plane (Frank Lapidus) drunk, thinking that will at least delay the flight (and the plane will miss the Island). Too bad: Seth Norris steps up. Widmore then fakes the crash footage. See, this fact always bothered me: why bother faking the crash footage when Flight 815 would've just been assumed to have crashed in open ocean? Rescue operations would've been suspended relatively quickly---no danger of rescuers accidentally stumbling across the Island. I think Widmore needed Dharma to believe that they had changed the past, that Flight 815 had no survivors, that the Hostiles would be without their generals in the coming war.

Just to be sure, Dharma operatives (again, still trying to change the past) have 2004-era Widmore send Keamy and his team to remove Ben Linus from the Island and kill everyone else. (In 2007, Ben Linus pretends to be a faithful Dharma employee who managed to survive the Purge, using this "cover" to infiltrate Dharma). Notice how there was a Dharma seal either on (or near, can't remember exactly) Keamy's orders in Season 4. However, Widmore sends the science team along as well, ordering them to turn off the gas, knowing that they'll eventually join the beach crew. (That's another thing that I never understood: if Widmore really wanted everyone on the Island dead, why bother turning off the Tempest gas? Widmore, not Ben, ordered the Purge. He could easily have just given his team gas masks, had them drag Ben away, and then use the gas to kill the rest of the Island population, if that was his real goal.) This is why Alt Dharma can't just gas the Others when they arrive on the ! Island in 2007.

Dharma thinks they've changed the past. That is, until their time-traveling operatives see the Oceanic 6 make headlines. Dharma then sends operatives to spy on them---to spy on Hurley at Santa Rosa, to get close to Sayid (and find out who the Hostiles' true leader is), etc. The "associates" of Widmore that Ben ordered Sayid to kill were really operatives of Dharma. Widmore freaked out at being seen with Sun because he didn't want to tip off Dharma that he and she are on the same side.

So the War between science and faith, between Dharma and the Others, has technically been going on since the beginning. And when Alt Dharma comes to the Island, they'll eventually summon "our" Widmore as one of their leaders---only to have him stab them in the back.