it is created by the "Machine", when it was release into the modern society, as a free entity, not being in controlled anymore, where practically everyone has some sorts of data on them online or in the database. This machine is practically everywhere, knows everything, well almost everything there is about Earth. Now this "Machine" is playing God amongst humans, where, Root is being trained as the leader of the organization by the machine, while the Machine also is controlling every single possible threat that makes it so that it power any less, for example Lifetrace, by using the organization it created. Like for example, when it started a fake company to write it owns code to have some memory from the day before, it was evolving.
Now, you would say why would the Machine would create the organization, and then give the number to people for the person who got killed in episode 2. Well, the machine has some sort of connection with it creator, so there is that one possibly that machine has two state, two faces, not necessarily good or evil, but more diverged among the choices they choose. Another thing is that Machine is able to argue with root, meaning it can makes choices.