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One of Cypher's most famous quotes from the movie is "Ignorance is bliss", which he utters while speaking with Agent Smith, referring to the state of people inside the Matrix.
Cypher may have been programming the console to automatically activate the data-needle at a certain time to jack himself in, and to auto-dial a hardline to extract himself at a specified time when Neo interrupted him.
When Cypher realizes that he is not the only one still awake, he immediately turns off all the monitors of the Operator console, preventing Neo from seeing what he was doing.