There is a third civilization that had a much darker tone attached and kept themselves out of the history books. They are chaos sorcerers that are now primarily peaceful because of the damage they had already caused to the world but they only number in the few dozens. The God was created as a counter to these people because of the potential threat and power they possessed.
The chaos sorcerors had not harmed anyone, the technological civilization wanted to get ahead of them and create a weapon to beat them. The God was created using research done by the technological civilization on the sorcerers. Might go into some details to say how the sorcerors got their power, might hand wave it away. The technological civilization had to go to the sorcerers and find out how to bind and split the God and contain their four parts into the stasis pods since they could not destroy them with the powers that they have. Later on in the game the player will have to return to these people to learn how to do it again.