A theory on everything but Jacob.
It's been argued that the submerged island, in what has been deemed our "flash sideways", is not a direct result of Juliet "detonating" the bomb. While I agree, there are many other aspects of the show that tie into this idea. While I do not have every answer, especially since all of our puzzle pieces of have yet to be revealed, I would like to present what I have built with those pieces already given to us. This does not give any insight into Jacob or his enemies, other than you should all go and read about the trapped brothers in the game 'Myst'.
In this post I will argue the following theories and propose new questions;
A.)Season 2: The true nature of the Swan 108 minute button protocol, fail-safe key, Radzinsky, Desmond's turning of the key and the Swan "discharge".
B.)Season 5: Dan's "plan" becomes Jack's & Juliet's "detonation".
Cutting through the fluff: Let us understand the first revealed hatch/station, the Swan, and it's complicated history. 197* The Swan/"hatch" is built by Dharma, and engineered by Radzinsky, who would later blows his brains out within the Swan while his partner Kelvin slept. Assuming this the truth (as Kelvin described it to Desmond), we can say Radzinsky eventually lost his mind or decided a.) not to deal with the events on the island b.)his drawing on the "blast door" was completed (either created out of insanity or with a purpose), and had no reason to live any longer. Or perhaps he could he have killed himself after suffering from being dislodged in time after the incident, like Desmond?
"Whatever happened, happened..."
In order for my theories to work, the following has to be true:
THE ISLAND "JUMPS" IN TIME BOTH MANUALLY (the "wheel") and ON IT'S OWN ACCORD.
Lets look at two events:
1)1977 Juliet's bomb and electromagnetic build up
2)Desmond's second failure to enter the code, and failure to turn the key in time (Yes, he failed!)
Could the island let Desmond fail in turning the fail-safe in time? Could it let Juliet detonate the bomb? Both outcomes would end up destroying the island. I believe in 1977 the bomb does not go off, it just causes or is replaced/combined with the electromagnetic energy discharge. Our original time jumpers jump again. But our 1977 Dharma folks are thrown about like Desmond after the hatch implosion (or quite possibly jump themselves. At some point, Dr. Chang knows about events from the future. See his lostpedia page). Both events caused by the same circumstances: the electromagnetic event and the hydrogen bomb dropped by Jack. Which was and always will be, underground at the swan. Dr. Chang survives and is injured as shown in our Orientation videos. Radzinsky must survive as well.
I believe the island jumped, in both instances. Either as a direct result to both instances, or to prevent those instances of occurring. Preventing a paradox, 'self preservation' if you will. Whatever happened, happened. Daniel knew this, which is why I'm not quite sure about his plan. Unless he calculated the bomb failing.
1977: The incident happens, our survivors disappear. Dharma folks at the swan are injured. There is probably an implosion/explosion similar to Desmond's "discharge". The swan is built as planned, but instead designed by Radzinsky to deter another event instead of research. How is this possible with 1977 technology? My guess is that it has to do with the bomb. The computer simply resets the timer on the hydrogen bomb which probably runs a bit longer than 108 minutes for safety reasons. He also creates the fail safe in the event that computer is destroyed or unable to enter the code. The code which they probably just picked from the stamped serial # on the hatch, which is probably willed by Jacob during a visit someone. The purge occurs. While Radz is on duty, he is the only known original Dharma survivor. I'll guess his work is not completed at the time of the purge, which is why the computer doesnt have automation. Not all Dharma can be assumed killed from the toxic gas. The! re were scientists all over the island. We do not know exactly when Kelvin joins Radz in the Swan, or how he gets to the island. It is definitely post Gulf War (1991) as per the information from Sayid's back story. The purge is suggested to have happened in the late 80's. So Radzinsky could have been down in the hatch for a few years by himself.
Side Note:
PILOT EPISODE and what we don't see: Desmond's first failure to enter the numbers, caused both the 815 crash AND the island to jump in time. When did we jump to? I don't know, but it will be revealed and have significance as all jumps do. We also have been led to believe the hatch discharge was from Desmond's turning of the key, but it actually was in Desmond's failure to do so that causes the island to jump itself again to 2004. Again: either as a result of his failure, and the magnetic anomly and Juliet's bomb, or the island's prevention of it. We see the flash in the sky as our new villain Ben holds Jack and company hostage on the dock. We are now back in 2004. Ben sends Hugo back to his camp and allows Michael to leave with Walt via boat and seamlessly return to their lives.
For the first 67 days on the island, unbeknownst to us, our survivors are not in 2004.