The military used the island to store atomic weapons.
The Dharma construction on the island was a costly, secret science station.
The military style food drops continue even after Dharma was eliminated.
The Widmore conspiracies on the fate of Flight 815 smelled like the cover-up of cover-ups.
This led many to believe before Season 6 that there was a secret or shadow government as a major actor in LOST. Our government funds a wide range of research, development, health, safety, and weapons technologies. All those aspects of research found their way to the island. L.O.S.T. could be code for "Land Of Scientific Testings."
“It’s All a Government Experiment” theory proposes that all the characters have all been brought here for a purpose, and the island is functioning as an elaborate Skinner Box to gauge their reactions. If this were true, some of the inhabitants of the island, probably the Others, know that it is an experiment, because they have information about the castaways and the outside world.
The discovery of the various hatches and the sketchy Dharma Initiative, which is still delivering food to the island, lend credence to this theory. When you look at why the castaways are on the island you will see that each of them has been told to get the flight by someone else or someone else’s influence has had them make that flight. The characters were corralled onto Flight 815.
So how can a government agency "stage" a chaotic mid-air plane crash just to get passengers to the island so they can conduct experiments on them? With the survival of a mid-air break-up nil, the idea of "drugging" the passengers and taking them to the island "sound stage" is more likely. There is precedent for this in the show itself: when Juliet was drugged then put on board a submarine.
The various Dharma stations lend credibility to the theory. The Hatch was a monitoring station for the unique EM energy field. The Pearl was a place where psychological experiments were conducted on people. There was a medical research facility where electromagnetic activity on the island may have studied as a was the cure of Jin's infertility, Rose's cancer and Locke's paralysis.
Theorists explain that in Season
3's opening episode, with the bear cages, it is hard to argue that there is not an experiment
going on there. Perhaps, the project began as experimental research on
animals, but when the plane crashed the islanders were finally able to
have access to research subjects that would model humans better than
anything else- actual humans. They may have had sporadic subjects prior to this
(Henry Gale, Desmond, etc) who seem also possible subjects. The Dharma
Initiative would have been the private contractor running the experiments. But then again, perhaps one experiment was how two different cultures, such as science and faith (the Others), would interact in a confined space (a litmus test for the Middle East perhaps).
Inman's involvement might also support this
theory. When he was in Iraq with the US Marines, he tells Sayid his torturing skills will be useful later. He would later wind up on the island in the Hatch with Desmond. He was
the last person on the island with Desmond, and he may have carefully
orchestrated the cover story of the "fake" 815 plane crash so Desmond could convince the survivors that rescue was never an option.
The series could center around experiments involving the Numbers, representative of
The Valenzetti Equation which predicts the exact number of years and months until humanity extinguishes itself.
During this Season 3 time frame, magazine interviews determined that most of the LOST actors personally thought this was the premise to the show. Harold Perrineau Jr. said, "I'd always believed the whole government conspiracy thing was great and then I heard that was the boring choice, but I thought it was really cool. But that's been my favorite one so far."
If each person was handpicked to be on the island, that’s a whole lot of planning and coincidence. If, however, each person is there by chance, the theory may hold even more weight.
What do many government funded secret projects have in common? National defense. New technologies from making better soldiers to new weapons systems. Examples of high tech include the sonic fence, the smoke monster, and even the submarine (how many private companies have submarines?)
The experiment could have been as simple as trying to determine if soldiers (Sayid) and criminals (Kate, Sawyer) could re-establish themselves in society; whether they can turn back their own selfish standards to help a group meet certain goals. It also could have been a ruse to send "dead" people through a dangerous experiment, such as the island as a time machine.
We saw that most of the research stations were closed or not functioning when 815 crashed on the island. However, that does not mean that the experiments stopped. Ben was still getting orders from a man called Jacob, his superior. Ben demanded lists, reports, information from his subordinates. He gave out deadlines. He demanded results. If the Dharma scientists were gone, why would Ben still be conducting research? The assumption is that the research never stopped.
But in the grand scheme of things, a government controlled island of human experiments did not give us any concrete results. What were the goals of the experiments? What were the results? Why were the main characters part of the experiment? If the main characters did not change their personal behavior, were the experiments a failure?