Jacob's motivation and the Alternate Timeline by DarrenKiwi70

Lost is like an Agatha Christie murder mystery...

All stories have a beginning, middle, and an end. In a murder mystery however, the story begins in the middle, with the discovery of the murder victim. The story continues with the detective searching for clues and identifying suspects.
The end of the story has all the suspects gathered together, as the never wrong detective reveals to all those assembled, and the reader, the beginning of the story...
i.e. The murderer, the motive, and the means of the murder.

As in a murder mystery, Lost begins in the middle with Oceanic 815 crashing on the island. Throughout the next five and a bit years, we've been presented with clues, red herrings, deaths and suspects. We are the detectives.
With the appearance of the Alternate Timeline (Henceforth called the LA-X Timeline), we are beginning to see, for want of better wording, the beginning of the story.

So here is my theory, presented in a murder mystery format.

The murderer- The one and only true candidate, Jacob.

The motive- Saving the island from being destroyed and sunk in 1977. Also to find a candidate to replace himself.

The means- Bringing or manipulating individuals to the island, to save it from destruction.

Theory:
I believe the LA-X Timeline is a Flash-Forward by Jacob from his Lighthouse of Mirrors. I think Jacob, shortly after the Black Rock event, discovers that scientists, decades into the future, will begin to drill into the Island, to tap into those pockets of energy, accidentally destroying the Island.
This is not the Incident. There is no one there to prevent the Island's destruction. It sinks beneath the waves, and the LA-X Timeline continues as presented in Season 6. This is the beginning of the story.

So Jacob is left with two choices. Let it happen, i.e. Let the Island be destroyed. Or, begin to manipulate individuals with the use of the Lighthouse, to prevent the Island sinking in 1977.

Now you may ask why Jacob, did not use his mojo to stop the creation of the Dharma Initiative, thus saving the Island. I have two possible reasons.

1. Jacob has only the ability to see Flash-Forwards and Flash-Backs tied to the Lighthouse. (Yes I think the Flash-Everythings we've seen since the first episode, was Jacob all along...the Peeping Tom.) So he is not omniscient. So Dharma was under the radar, as far as Jacob was concerned, until he saw the drilling and the end result.

2. Dharma served a purpose as well to Jacob. Time travelling Faraday joined Dharma in 1974, and pretty much devised the theory of using a nuclear device to counteract the explosion of energy, thus providing the solution to Jacob's problem.

Supporting Evidence:
1. Ethan Goodspeed's presence in the LA-X Timeline.
We know Ethan was born within a few days of the Incident in the Oceanic Flight Crash Timeline. We know he survived the Incident and becomes a member of the Others. In the LA-X Timeline, I believe Horace was never a part of Dharma. Ethan was born in the outside world, so he was not on the island when it sank.

2. Ben Linus's presence in the LA-X Timeline.
We know Ben was recovering with the Others when the Incident takes place. Somehow he is returned to Dharma, who he eventually betrays and becomes the Leader of the Others. In the LA-X Timeline, since Horace never joined Dharma, neither did Roger Linus. So Ben was not on the Island when it sank.

Acknowledged Counter Evidence:
In the LA-X Timeline, the Island doesn't look like it’s been underwater for 27 years.

Conclusion:
I think Jacob manipulated individuals, solely to stop the destruction of the Island.
1. He got a Hydrogen Bomb to the Island
2. He got Horace into Dharma. A sympathetic Leader, Horace allowed Sawyer and friends to stay on the Island, and who got Faraday into the Dharma Initiative.
3. He brought in a motivated Jack to lead his fellow Losties, in executing Faraday's plan, which ended with Juliet saving the Island by detonating the bomb.

There were downsides and risks that Jacob recognised, that MIB could exploit, including the hapless Ben and clueless Locke, who were drawn into the thread that Jacob was spinning. Jacob probably saw his death coming, and went to ground after the Incident, hoping to protect his replacement, whomever that maybe. Stay tuned.