Following another theorist’s proposal that the Island is a macroscopic place in which multiple quantum states can coexist: Just as Schrodinger’s cat is both alive and dead before an observer checks the experimental result, two states of the universe exist at the end of the events of ‘The Incident’: one in which Juliet detonated the bomb by hitting it with a stone, and one in which she failed to do so with the stone and died shortly thereafter at the bottom of the Swan drill-shaft. Juliet, in effect, committed quantum suicide. She was motivated to strike the bomb due to her regret over Sawyer's love for Kate (Fate), and she was able to ignite it due to the quantum behavior of the bomb (chance). The unpredictable outcome of the meshing of the Swan EM and Jughead energies is the sustained existence of the sideways universe.
Recall, for a moment, the Season 3 episode ‘Flashes before your eyes’ when Ms. Hawking told Desmond that pushing that button is the only really important thing that he would ever do? The button was ‘really important’ because it held at bay the profoundly important event that really did occur in the sideways universe—the sinking of the Island. The Island’s unique properties—its tendency to move within space and time, the buffer of warped space-time surrounding it (think Faraday’s projectile experiment, and the timeslip sickness experienced by Minkowski, Desmond, and others on the Kahana) emerge from a stable equilibrium between the real world and the unique EM sources underlying the Island, especially the massive source at the Swan site. When the DI drilled too deep at the Swan, they breached the anomaly, an act with massive, unforeseen consequences. The Island-world equilibrium was upset, and thus the Island fell to the bottom of the sea.
Let's talk about the universe where Juliet failed to set off the bomb. We'll come to know it as the Sideways universe. Though the bomb didn't go off, the chaos started by the Dharma drilling continued, leading to the island sinking to the bottom of the Pacific, as we saw it in the opening of ‘LA X’. Jack, Kate, Sawyer, Hurley, Jin, Miles, and Sayid...they all died either at the Swan site, or in the aftermath of the EM anomaly breach. At least Ellie, Charles, Roger Linus and Ben Linus were able to escape the Island before it sunk. Richard...may have died on the island, or not. For now, let's assume he did. Penny was born before 1977, so she'd be a young girl awaiting Charles and Ellie when they return to the mainland from the doomed island in 1977.
However, Ellie has brought with her from the island the notebook of the young man she shot who claimed to be her son. She will study it backwards and forwards in the years following 1977. She pieces together, from the notebook, some, but likely not all of the events of the life of Daniel Faraday as we knew him. She knows he was her son, that he was a time traveler, that he lived a post-1977 existence that was not happy, that 'Desmond Hume' was his constant, and probably a lot more—Faraday always said that everything he’d ever learned about the Dharma Initiative and about the Island was in his notebook! So, in the years following 1977, Ellie learns that she was, somehow, able to both kill her son and avoid doing so. She keeps this knowledge, very, very close. Perhaps she’s told her husband Charles, but just as likely she hasn’t.
Thus, when Desmond Hume starts asking about a 'Penny' (a name that may also have been in Faraday's notebook), she knows that this is an unnatural event, a violation, and wishing to preserve the gift she's been given of a 2nd life for her son, she attempts to quash Hume's questioning. All of the Sideways versions of the 815ers that we’ve seen in Season 6 are simply the grownup versions of the off-island child-versions of these characters that were growing up in the real world in 1977.
Let's move on to the alternate universe, in which Juliet successfully set off the bomb. We know this as the main timeline of Lost that the characters have experienced in Seasons 1-5. When Juliet ignited the bomb, Richard and the rescued Ellie were watching from afar. They knew that Jack, Kate, and Sayid (though I can't remember if they ever saw Hugo, Jin, Sawyer, or Juliet) were right at the site of the explosion.
Being at ground zero of a nuclear blast typically results in your death, and that’s why Richard tells Sun that he 'watched her friends die’ when she asks him about the Dharma yearbook photo at the end of Season 5. The bomb did not destroy the Island. In fact, it’s destructive radius is limited to a very small space around the Swan site due to its reaction/negation with the EM energy at the Swan. After the bomb was detonated, the DI eventually fills in the Swan site with concrete and builds the Swan hatch. It is the residual radiation of the bomb that leads to the problems that pregnant women face on the Island after 1977.
The Swan, until Desmond turned the fail-safe in 2004, acted as a ‘cork’ upon the EM energy beneath. In this timeline, Ellie leaves the Island knowing that it’s stable, but that its safety is very precarious. Unless the Swan site is constantly attended, the EM anomaly will escape and the Island will be destroyed. She is (for reasons that remain unrevealed at this point) absolutely dedicated to keeping the Island safe. As she reads the journal of the young man she shot, she realizes that he was indeed her son, and that it must be her heavy burden to guide him on a path that leads forward, and then back in time, so he can be sure to set off the H-bomb and prevent the DI from destroying the Island. From Daniel’s journal, she’s able to learn something of Desmond’s involvement with the Island.
It’s Ellie who passes this information to Charles, and it’s she he refers to when he tells Desmond ‘If everything I’ve been told about you is true, you’ll be perfectly fine.’ before he zaps Des.
WHACKADOO PREDICTIONS AND COROLLARIES ARISING FROM THIS THEORY:
1. Remember when a visibly distraught Ellie stepped into the living room where Daniel was playing piano in ‘The Variable’? I predict we’ll see this scene again from Ellie’s point of view. The reason she’s distraught is that she’s gotten off the phone with Charles, and they’ve agreed that Daniel is now old enough that he must be manipulated into becoming the man who will eventually return to the island and die at Ellie’s hand.
2. We will also see a scene in which Richard and a dazed Ellie watch a mushroom cloud arise over the Swan site. Ellie will be holding Daniel’s journal.
3. Ellie has fulfilled her 3 key tasks after she has (i) made sure Des doesn’t marry Penny, (ii) convinced Daniel to take Widmore’s Kahana offer, and (iii) sent (most) of the O6 back to the island on Ajira 316. This is why she tells Penny that ‘For the first time in a long time, I don't know what's going to happen next.’ She maintained the time-loop that kept the Island from sinking, presumably in the service of something that’s ‘bigger than her’.
4. The intersection of the two realities is the September, 2004 flight of Oceanic 815. It’s chance alone that leads Charlie to experience his vision, but it is destiny/Fate which motivates him to lead Des to a road to Damascus moment.
5. Main timeline Ellie *does not* know about the Sideways Universe. In fact, the only main timeline character (with the possible exception of Flocke or Jacob) to know of the sideways universe is Des.
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