I am a bit lost. How is cryptography about secrecy of the text through some operation, like a function, while at the same time being a system that defines itself?

Cryptography has nothing to do with secrecy at all. It has to do with maintaining the integrity of the communication (or specifically, the message) given highly active and adversarial entities.

Anyone who thinks they can have security through secrecy (i.e. 'cryptography') is a fool, imo.