Cypher clearly represents Judas in the Christ story embedded within the Matrix. He is the only crewmember with facial hair, and the only crewmember who says anything to Neo when Morpheus introduces the crew to him. Just as Judas betrays Jesus with a kiss, Cypher betrays Neo with a sneeze. When Cypher wears the operator headset, it makes him look like he has horns on top of his head, like the devil.

When Neo talks to Cypher on the Nebuchadnezzar (and when Cypher meets Agent Smith in the Matrix), he is wearing green, showing his desire to be plugged back in to the Matrix. I even speculate that the ribbed pattern (on both green shirts) is symbolic of Matrix code. When Cypher is inside of the Matrix, he gives Neo a smile of guilt while a reflection on his sunglasses makes him look like he has the eyes of a demon. And when Cypher starts unplugging crewmembers, he is wearing a red shirt with a tear in it, making him heartless.

During Cypher's conversation with Agent Smith, Cypher says:

Cypher: I don't want to remember nothing. Nothing. You understand? And I want to be rich. You know, someone important, like an actor.
Agent Smith: Whatever you want, Mr. Reagan.

Remember that President Ronald Reagan was an actor, was rich, and had Alzheimer's Disease.

Also, just as Agent Smith refuses to call Neo anything but Mr. Anderson, he also refuses to call Cypher anything but Mr. Reagan.

How exactly does Cypher pull off his betrayal?

First, Cypher calls Trinity and allows agents to trace the call:

Trinity: Did you hear that?
Cypher: Hear what?
Trinity: Are you sure this line is clean?
Cypher: Yeah, of course I'm sure.
Trinity: I better go.

Cypher betrayed Trinity to the Agents as proof that he is a real informant. Even though Trinity got away, we see that it works after Agent Smith crashes the truck into the phone booth:

Agent Brown: She got out.
Agent Smith: Doesn't matter.
Agent Brown: The informant is real.
Agent Smith: Yes.
Agent Jones: We have the name of their next target.
Agent Brown: The name is Neo.
Agent Smith: We'll need a search running.
Agent Jones: It has already begun.

Next, Neo startles Cypher when Cypher is typing in front of the Matrix code screens. Cypher quickly looks around then shuts the screens off, relieved that Neo has not yet been taught how to read Matrix code. Clearly, Cypher is setting up the meeting with Agent Smith to negotiate his reinsertion into the Matrix (that scene immediately follows the scene of Cypher's conversation with Neo).

When Cypher meets with Agent Smith, he is obviously able to jack himself in and out of the Matrix without the help of an operator. A scene from the video game ETM shows Trinity and Ghost in a simulation together (scenes from this game were filmed at the same time that M2 was filmed). When they are finished with the simulation, they both take their head devices off, which indicates that they were able to end the simulation from within the simulation. Also, in Matriculated (The Animatrix), we see people plug themselves into their virtual reality program.

But we didn't actually need those examples anyway, because it just so happens that the Wachowskis clear this up themselves in a chat session they held with fans:

WachowskiBros: ...Cypher, at the beginning of this scene, is setting up an automated system to allow him to go meet with Agent Smith.

This probably means Cypher is setting up an exit phone to automatically start ringing at a specified time, along with an auto-jack-out program to load his consciousness back into his head as soon as he puts the phone up to his ear.

Just after Neo, Morpheus and the rest of the gang go to see the Oracle in the Matrix, Cypher drops his phone into the garbage can as it dials the Agents. We see Cypher twitching in the real world. That gives the Agents time to sabotage the exit location.

After everyone falls down the wetwall of the building after being trapped, Cypher pretends to not be able to get up and go with Trinity to escape the authorities after they fall down. Cypher is captured and taken away, and the Agents manufacture an accident that allows Cypher to get away and find an exit from the Matrix quicker than the others do. This way, Cypher can unplug the rest of the crew to minimize the chances of interference while the Agents try to crack Morpheus's mind.

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