The more missions you complete for an Overarch, the more they will trust and respect your character. Of course, that trust will be weakened if you work for the opposition or fail too many missions. The player has the option of converting the trust into an official position within the Overarch. Overarchs are not so naive as to expect loyalty from their Alphas but they do their best to encourage it and will not tolerate active treachery for long. This gives them access to the missions created by their parent organization, the training and the special equipment, but allows the characters and players in the group to prove their abilities as a semi-independent entity.
Players can also create their own completely independent groups.
The Overarchs and other organizations in the game will react to them in a believable way. If a member consistently acts against an Overarch, the Overarch will respond accordingly to the individual and the group. These groups can define their own cause or causes and individuals can compete to gain the greatest status within the group. Both groups can build up their own individual headquarters, and create a pool of items and other resources. As the group gains in fame and reputation, the members will gain a boost to their renown based on their own standing within the group.