Cryptos was a Zionist captian during the war against the Machines. He was one of the few captains who were in Zion when the other hovercrafts were destroyed by Smith. He was seen by his peers as an extremist, believed to have once requested the use of virtual nukes to destroy the Matrix (which would in turn kill all the bluepills).
After the war, Cryptos disappeared; it is believed this is when he turned into a Cypherite. No one knows if he left on his own accord or was taken by force, but we do know that he had turned from a Redpill activist to a Cypherite or Bluepill wanna-be. Cryptos is believed to be the leader of the Cypherites although no one knew about him until after Veil was released from her prison and rejoined the Cypherites.
More recently in The Matrix Online, Cryptos was attacked by Seraph for reasons currently unknown. This attack left Cryptos blinded, and revealed that Cryptos was under the control of the Machines. This revalation has created a rather tense situation between Zion and the Machines, as this revelation is viewed as a direct violation of the truce formed by Neo.
- Cryptos' name is probably based on the prefix "crypto-" which means "secret or hidden"