To decipher meant to discover the meaning of or to decrypt something.
In 2268, Commander Spock spent fifty-eight days trying to decipher obelisk symbols which were a highly advanced form of cipher writing. After being prescribed rest by Doctor Leonard McCoy, Spock later discovered that the symbols on the obelisk were not words but rather musical notes, and the tones corresponded roughly to an alphabet. (TOS: "The Paradise Syndrome")