Lost At The Temple:

Lost At The Temple: Diary of a mad LOST fan
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Alternate Timeline Theory of LOST. Posted by James721

The alternate timeline honors the paradox that created it.
In it's split to 2 different realities, the alternate universe is pre-existing [1]. However it is the soul [2] and its spirit [3] that 'combines' the two realities by a common thread; the birth of a shared soul.

The soul originates at birth where as the spirit pre-exists but linked to specific souls (perhaps this has something to do with the names ans attached numbers on cave walls). The soul is however separate from matter and does not adhere to the nature of time. Its energy resides however in matter whereby this matter is bound to the earth (MIB and JACOB). The spirit is the original character and force that both animates the soul(s) and gives behavior to it's nature.

Here in Lost, the Island is the Spirit for both MIB and Jacob held in some sort of balance. When the MIB soul(s) leaves the island it sets off the balance with its controlling spirits and causes the island to sink. I could see how MIB and Sawyer leave the island in current time (timeline A) by turning the wheel together and going to the alternate timeline 2004. This sends them AND everyone and the inland to the alternate timeline... or so it seems, as it actually brings the two timelines back together. Boom! -Sawyer is now on the plane as himself in the alternate timeline with no memmories as are all the other Losties (and people on the island) and puts them wherever they would be in that alternate reality / timeline, which NOW we would view as timeline A.

Voila Smokey(MIB) has succeeded and is now free and Jacob is trapped as a soul outside the realms of the spirit if the island which is now underwater. He somehow uses the spirit of the island as the Losties fly over the island in the alternate timeline. We see this, from the point of view of the camera (S6E1), leaving the plane and traveling through the clouds and plunging into the water then swimming to the foot on the sunken island. I believe that this is the soul of Jacob, now separated from Sawyer, as Sawyer previously assumed candidacy of jacobs soul before fleeing the island with MIB. Jacobs soul it reunites with the spirit of the sunken island.

('m losing it!)
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my own references:

[1] my pre existing alternate universe the pre existing alternate universe model in my idea follows either of 2 possible formats:
{A} many branches timelines model ": Like a tree time begins with one stem then splits to many, then splitting again in time growing to an infinite number of branches with some dying off while others grow and 'branch out' In this instace the possible chices of life can pre exist in each of heir own respective timelines as the branches grow.but only from the poinsts in time (or points along a branch where it spleites ) that present choices or options.

{B} my "Ray of light timeline theory". Time begins from a single point like infinite rays of light in all directions and travels outward during time. As time moves. each ray of light is a timeline, with a complete pre-existing futute and past. Where you are on the light ray is the present. A ray of light holds you suspended on its path UNTIL you decide to select a new path or ray of light to travel on. In this theory all the choices and paths infinitly exist.

[2] crazy LOST Soul theory:
The soul is separate from matter. It is reliant on matter to exist in time. It's energy resides in matter. The soul maintains memories that can be transferred via amplified vibrational energy.

[3] crazy LOST Spirit theory:
The Spirit is the source that drives the soul and does not rely on matter to exist. The spirit sparks the soul at its beginning. The spirit is able to exist in both timelines and in multiple relaities simultaneosly. The spirit communicates to the soul in all realities and can plant a memory from an alternate time and space experience from past or future, by communicating vibrational energies from complex patterns used in driving the soul.