The Matrix Theory: The Oracle Told Cypher To Turn On Morpheus
To begin with, after he has gone back into the real world and is killing off his teammates, Cypher straddles Trinity’s jacked-in body and tells her over the phone: "You know, for a long time, I thought I was in love with you." There were implications throughout the film that before Neo showed up, Cypher and Trinity were an item. Maybe it was just Cypher making the moves on her to no avail. Regardless, once Neo shows up, Trinity shoves Cypher to the side and has eyes only for Neo from then on.
The next clue comes when Cypher then straddles Morpheus’s body and says, “God, I wish I could be there when they break ya. I wish I could walk in just when it happens so right then you’d know it was me.” Cypher has a profound disdain for Morpheus, and he was in love with Trinity. These two things point to the possibility that, before Neo, Morpheus freed Cypher from the Matrix believing him to be the One. But Trinity didn’t fall in love with him, nor did he prove to have any superpowers like Neo. So after they discovered Cypher wasn’t the One, he was just stuck in the real world where he didn’t want to be, and during that time he built up a grudge against Morpheus. When he says the line, “All I do is what he tells me to do,” he is expressing this resentment because he thinks, had he been the One, then he would be in charge and Morpheus would have to follow his orders.
Our final clue is simply his name. The word “cypher” means “a secret or disguised way of writing,” or otherwise, “code,” which obviously plays heavily into the computer network aspects of the film, but it could also mean cryptic message. Now here’s another one for you: the word “cypher” can also mean “zero,” which may signify Cypher and Neo as opposing parts to a binary code; Neo is the One, Cypher is the Zero . . . or in other words, he is not the One. But he is also an equal and necessary part of this binary.