The name Cypherite or, masked men, has been added to the list of other terms such as Judas, traitor, Benedict Arnold and other names and terms meaning betrayer. But we tend to forget the seeds of this weed now strangling us all who were chosen wisely and carefully and where this weed is headed now.
Zion, the only organization that has an active focus in turning the blue into the red. During the war, most likely threw all of its incarnations, Zion was very careful in who became a red, a "freedom" fighter. This process usually entailed a period of observation of the potential. During this observation, the reds watching said potential would closely moniter how well the subject accepted The Matrix, if the subject completely believed in the "false" world then the reds would move on to another potential and no harm, to both the red or blue would be done. However, if the subject displayed a questioning of this world known as The Matrix then they would move to first contact.
First contact would be done any number of ways, the most notable of first contact would be in the case of Thomas Anderson encountering Trinity in a still unknown club. This was followed by second contact, a phone was delivered to the subject in which the communicator, in this case was Morpheus, instructed Thomas Anderson in how to evade capture (which in this case proved futile) and eventually how to meet them for his extraction.
After extraction, the newly created red would be subject to medical procedures such as removing of the hardware plugs the best they could and the rebuilding of the atrophied muscle structure. Then came the "orientation" in which Zion would tell their side of the war.
After the war in this era of truce we now live in however, Zion seems to have abandoned the practice of carefully selecting minds that could withstand extraction but had a desire to leave in the first place, rather they seem to hand out the redpills to whoever seems curious and the results now speak for themselves.
As a result of this new awakening policy, a large percentage of reds that should never have been awakened now walk among us unable, or unwilling to accept the fact of the real. They now have a seemingly uncontrollable desire to return to the matrix and have it as if nothing has happened. They have done some rather unspeakable crimes such as the destruction of entire hover barges, assassinations in the real, and countless others. All in the name of returning to the matrix.
However, a very strong, and every major question must be addressed and that is how do they intend to return to the matrix in the first place? Their spokes person, Cryptos, when he speaks hints strongly of machine ties. Preaching making their beds and whatnot, this leads me to believe that an alliance between the machines and cypherites exists or, the leadership of the cypherites has been misleading it followers into believing that there is a way to return.
If a alliance exists, then the question of why comes to mind. Why would the machines agree to allow the cypherites back into the matrix after killing, attacking, and what not? One possible answer is that Zion continues to draw from the blue population at an alarming rate that the machines seek to slow it down by using the cypherites as a sort of secret canon fodder, attacking Zion and attempting to draw them away from awakening so many minds. Or they may attempt to slow down the rate of energy loss by reinserting the cypherites, though this view is less likely as it would only serve as a very temporary measure and the return would most likely be slim to nothing at all.
The other possibility of the cypherite leadership misleading the followers seems more and more likely when one considers the situation of a typical cypherite. They want to return so badly and not remember a thing that they are willing to do anything. This opens them up to a charismatic leader or leadership that promises them that they can return to the matrix in exchange for the above mentioned acts of terrorism.
In closing, while the source of the cypherites is and continues to be Zion, their future may quite possibly lay with the machines. If this is indeed the case, then the machines have already broken the truce.
