it wasn’t uncommon for agents to join the protocol, nor was it uncommon for them to have special abilities. However Cypher never would have expected one to join with a godlike being.

eventually it came to a few years of you being there with the protocol and your claimed human before tragedy struck.. one day the human was gone, nothing for Sage to revive or Omen to find.

so eventually Brimstone talked Cypher into trying to be claimed by you.