The Deltite used The Encoders for Project Delta. Their purpose was to replace S.H.I.E.L.D. agents with Deltan-model LMD's which were more  sophisticated LMD's born from artificial wombs. The Deltite maintained control over The Encoders by creating a religion for them. The Encoders turned on The Deltite because of his efforts to become more human. They believed he was betraying their religion. They were all eventually destroyed aboard the SHIELD satellite.