I'm toying with the idea that the "He" that Mr. Friendly and the other Others report to is Henry Gale.

He appears to be a master manipulator / psychologist.

Maybe he controls a faction, the remnants of a long term and mostly failed Utopian experimental society. His method of control? Fear of the virus, and control of the vaccine supply.

But there are some cracks. Ethan shows a few signs of independence, taking Claire out for a walk, and expressing his wish that she could stay with them. I think Ethan was pushing his bounds by telling Claire as much as he did. Alex obviously undermined the plans of the Others, but still stays with them - they must have some way of keeping her around.

And one more observation. If Henry is an Other, why is he not too concerned with being locked up in the Hatch with no access to the vaccine? Perhaps he knows the sickness is bogus, or is only contracted on purpose (i.e. by an injection), or he personally is immune for other reasons.

... rough thoughts ...