Who were the hands of blue?

The Hands of Blue are the individual contractors to the Alliance. They are the closest the Firefly series has to a main antagonist. They are never referred to by name, only by River as the "Hands of Blue". Many have called the individual members "Hands of Blue 1" and "Hands of Blue 2".

The Hands of Blue are two mysterious men with blue gloves. They are most directly involved in the Alliance's darkest secrets and their biggest operations. Their objective was to find River Tam and her brother, Simon, to prevent them from discovering and revealing what River knew; that the Alliance inadvertently created the Reavers, which the Alliance did not want anyone to know, in order to seem the perfect government to its subjects.

Jayne briefly decided to turn on the crew of the Serenity in the episode Ariel; he called the federal agents, led by Agent McGinnis, in order to receive a reward, when Simon was on the planet Ariel to find out what the doctor at the Alliance's academy did to River. The Hands of Blue arrived. When they found out that McGinnis talked to River, Hands of Blue 1 used a sonic device, causing McGinnis to bleed from the nose, eyes, and mouth, eventually killing him. He killed another federal officer this way when he saw that he was still alive and merely wounded, showing how evil they were by killing their own men.

Eventually, in the comic Serenity: Those Left Behind, they teamed up with the former federal agent, Lawrence Dobson, who wanted revenge on Malcolm Reynolds for shooting him in the eye, which he and the other crewmembers believed to have killed him. They attempted to find Simon and River while Dobson attempted his revenge, but was killed when Malcolm shot him in the head. The Hands of Blue approached Serenity in their ship, but the entire crew got on board and when Wash took off, Mal told him to "step on it", so that Serenity's jet flare hit the ship directly and incinerated the Hands of Blue, leaving only their skulls.

Following their deaths the Parliament sent the Operative to find Simon and River.

one of the biggest unfinished storylines from the series are the mysterious villains that river calls "two by two, hands of blue" they struck so much fear in the minds of the viewer like they did for river. but then the series was cancelled and they didn't come back in the movie (serenity). I think that they might have never existed. and that they are only a manifestation of river's fear and psychic powers. ofcourse the obvious guess is that they are operatives like the one in the movie. but they seem like tailored to rivers fears and anxieties. they wear gloves like the people that did experiments on her. they seem soulless.

they are seen first in the episode. "the train job" as they talk to the alliance colonel and start their "hunt against the tams. this could totally be in river imagination as that scene doesn't affect the rest of the characters.
but then they play a bigger role in "Ariel" as they infiltrate the hospital and leave behind them a trail of bloody bodies using their sonic weapon. meanwhile river feels their presence and as she gets more scared, they get more ruthless. I think she not only made them up but using her psychic powers is planting the idea of them into the minds of everyone that "sees" them. she makes other people see them and than they shortly die after because she killed them with her mind. she only explains it to herself by saying they have the sonic weapon. then they never show up again. they only come when river is most vulnerable. she hates hospitals and the whole mission in ariel was a big p.t.s.d trigger for her that made them real. after that episode she starts the road to recovery and they never show up again.

These two blue-gloved men (agents of the Blue Sun Corporation? The Academy? the Alliance?) are pursuing River after her escape from The Academy. They always appear as a pair ("Two by Two"), have a generally creepifying demeanor, and wear blue gloves at all times.

We were introduced to the Hands of Blue in The Train Job and met them again in Ariel.

The Hands of Blue have access to advanced (or, at the very least, cutting-edge) technology and equipment (as seen with the shuttle and HOB Rods they use in Ariel).

The Hands of Blue were last seen in the short comic book series "Serenity: Those Left Behind", wherein it was revealed that their "gloves" did in fact extend under their clothing and were in actuality some kind of full body suit. It is evident that this revelation was not left over from the TV series as on the DVD commentary Joss Whedon himself admits that he just wanted them to wear the blue gloves and had no reason for doing so other than aesthetics. The pair also met their end towards the conclusion of the limited series when their ship was badly damaged by Serenity's full burn. The last few pages depict the passing of their mission onto the Operative whose superior refers to the Hands of Blue as private "contractors".

Theory of origin

It is possible that the Hands Of Blue are an earlier-generation version of the... creatures that children like River were being modified to become. Alternately, they may be partially-failed experiments -- it's clear that it is only River's inherent genius that allows her to process all of the information that she is subject to, now that her mind has been modified -- in a less-apt subject, that input would be overwhelming and further mental modifications (very much like a lobotomy) would be necessary to prevent psychosis from setting in entirely. Certainly, the unusually calm, unemotional behavior of the Hands of Blue is reminiscent of the behavior of certain types of lobotomy subjects, or a sign of advanced anti-social personality disorder such as sociopathy, or the more notably lethal (as appropriate in this case) psychopathy.