Since he's also an agent of the C'Tan - or at least he used to be.
Based on what? Cypher used to have a C'Tan phase sword, but so do Callidus assassins. In his hero and villains spotlight yonks ago, it was explained that he lost that same C'Tan blade battling the Necrons...

Cypher has never had an unambiguous motive given for him. So a theory that he was an agent of the C'Tan could make sense, and still include him losing his blade since the C'Tan have a lot of infighting, but you're stating it in pretty bald terms.