The Ethos
If you didn't already guess, this section contains spoilers.
The Ethos' Establishment
After the great war 500 years before the time of the game, Solaris decided to implement a more direct system of controlling the land dwellers. This was the Ethos. Divided up between the land of Ignas and the islands of Aquvy, the members of the Ethos managed the land dwellers under the guise of a religious institution. The Ethos was also the only organization that officially repaired Gears. However, the true purpose of the Ethos was to manage the activities of the land dwellers and to serve as a go-between from the land to the floating city of Etrenank, the Solarian capital. The Ethos regularly sent shipments of supplies and "human resources" (land dwellers to be used as manual labor) to Solaris. Many of the people sent there were people who came to the Ethos for spiritual guidance, unless they became Etones like Billy. The Ethos also collected and stored battle data from the Kislev Battling arena and wars (such as the one between Kislev and Aveh) for future use.
The Bishops
The Bishop class were the top-ranking members of the Ethos, aside from the Pontiff. Shakhan, although believed to have been excommunicated from the Ethos 19 years before game time, was actually still a bishop and reported his activities in Aveh to the Ethos regularly. It's kind of hard to explain the bishops' roles in more detail, because some knew more than others about the real purpose of the Ethos. In general, the bishops weren't fully aware of the Ethos' direct connection to Solaris or the fact that Solarian agents such as Stein also worked within the organization. That's why they believed they could break away and become independent (more on that later). However, Stein (and possibly a few others?) used his position as bishop to move about on the land without suspicion, while in reality he was a loyal agent of Solaris and mostly used his position in the Ethos as a front for his activities.
The Role of the Etones
Everyone pretty much knows that an Etone's job was to exterminate Wels, but what was the real story behind all that? Wels were actually people at some point. The M, or -Malakh-, Plan included mutating humans into Wels, which were also spare parts for Deus. The Etones were sent to kill these mutated people that were sent to the earth, most likely as another ruse to get the people to believe the Ethos was around to help people and at the same time to dispose of the Wels when they were no longer needed. (The purpose of the Wels, or at least one of them, was to be test subjects for the process of fusing people with Gears. If a Wels proved worthy, it was fused with a Gear. If not, it was terminated.) However, they weren't really doing a wrong deed, if you think about it. Wels suffered an excruciating amount of pain, and attacking humans served to ease it for a little while. The only real way to ease the pain, though, was to put them out of their misery, so the Etones were actually saving people in that respect. However, although Billy had yet to find this out, the Etones served another purpose as well. Stein himself formed the Etones as a sort of internal affairs organization within the Ethos. If any members were found to be "undesirable elements," they were taken care of by the Etones. Verlaine, one of Billy's friends, knew of this and told Billy about it in the Ethos headquarters before Stein showed up and killed him.
Downfall of the Ethos
So why did Solaris send assassins to murder everyone in the Ethos? Simply put, the Ethos was trying to break away from Solaris and take over the world on its own. Working on its own and not reporting any of the findings to Solaris, the Ethos had discovered the ruins of Zeboim, which contained ultra-ancient and very advanced technology. The Ethos planned to use this technology to its advantage in a breakaway from Solaris and ultimately to dominate the world. Of course, some members of the Ethos being Solarian officers first and foremost, Solaris found out and had the Ethos eliminated.
...But isn't it weird how even after that, there are still Ethos workshops everywhere?
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