My eyes are buggy after a long day at work, so I’m not sure if anyone else has posted this theory yet but…
The way I see it is that the DI was started in the 70’s (as far as I can tell from the videos - especially from the Lost Experience). They set up the island, with all the hatches, and took a bunch of people there - scientists, volunteers, etc - to live and work in their experiment. I suspect DI also set up the village (the houses where we saw the book club meeting and such) where the Others now supposedly live. That is where the DI workers lived when not working in the hatches.
Something went down and some of the DI people - possibly the workers themselves but I am guessing un-willing volunteers who came as children, family members of the workers, etc - decided they didn’t want to do these experiments anymore. They didn’t like how Dharma was running things. I’m guessing some of the mind experiments may have gone bad, too. People were scared of the “Tree Crushing Monster.” All sorts of stuff that could have turned people away. There was, in effect, a mutiny.
Like any good mutiny, there has to be a leader and some hierarchy. Ben - who I suspect came to the island, unwillingly, as a child - became the leader of the new splinter group. They became known to DI as “The Hostiles.”
The Hostiles used kidnapping to further their cause. I’d imagine they gave people like Ethan an ultimatum - come join us or die. This mutiny went on while there was still communication with Hanso/DI, hence the “hostiles” information on Locke’s chessgame video.
So now Ben’s running the show. 'Cept he’s gone through a lifetime of weird DI experiments, so he’s a little nutty himself. He starts setting up his own experiments (Daryl (Alex’s boyfriend…that his name?) in the room with the images, the human cages, the surgery center, etc.
The Patch Guy…seems like he’s an original DI worker who was stronger than Ethan when it came to resisting the Hostiles, so they did indeed let him hang out in his own place but since Ben is pretty much World Leader here on the island he still has to live by their rules. Ben can control how much of a connection anyone has with the DI. So Mikail is trapped there reluctantly. He doesn’t care if he lives or dies now because if he makes it to Ben he’ll probably get killed anyway.
Why was Miss Klugh there too? She could be a go-between between the Hostiles and Mikail. She could be guarding him. She could have been in charge of that hatch. She could be a reluctant DI disstenter like Ethan and Mikail.
So to wrap up this rambling…
The DI produced the Others, and the Hostiles = the Others. There’s just no one left who is faithful to the original Dharma Initiative. Ben is the new Alvar Hanso.