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Just a theory, really.

Could it be that Trinity had given up hope on finding the Chosen One and Cypher convinced her to be his operator while he made a deal with Agent Smith?

Why I think it's possible:

There is an unclear history between Cypher and Trinity. Maybe he made an advance and she rejected him, but was still interested in going back to live in the Matrix.

MAN (V.O.) Yeah?

WOMAN (V.O.) Is everything in place?

TRINITY (WOMANV.O.) I said, is everything in place?

CYPHER (MANV.O.) You weren't supposed to relieve me.

TRINITY (V.O.) I know but I felt like taking a shift.

CYPHER (V.O.) You like him, don't you? You like watching him?

TRINITY (V.O.) Don't be ridiculous.

CYPHER (V.O.) We're going to kill him. Do you understand that? He's going to die just like the others.

TRINITY (V.O.) Morpheus believes he is the One.

CYPHER (V.O.) Do you?

TRINITY (V.O.) I... it doesn't matter what I believe.

CYPHER (V.O.) You don't, do you?

TRINITY (V.O.) If you have something to say, I suggest you say it to Morpheus.

CYPHER (V.O.) I intend to, believe me. Someone has to. The final NUMBER POPS into place --

TRINITY (V.O.) Did you hear that?

CYPHER (V.O.) Hear what?

TRINITY (V.O.) Are you sure this line is clean?

CYPHER (V.O.) Yeah, 'course I'm sure.

TRINITY (V.O.) I better go.

In this scene, Trinity seems to snidely remark on Cypher's regard for Neo.

CYPHER There's something about him, isn't there?

TRINITY Don't tell me you're a believer now?

CYPHER I just keep wondering if Morpheus is so sure, why doesn't he take him to the Oracle? She would know.

TRINITY Morpheus will take him when he's ready.

Maybe her coldness towards Cypher was an act to protect Neo and atone for her transgressions.

closed as primarily opinion-based by tilley31, Ward, Valorum, Chenmunka, SQB Nov 4 '16 at 9:33

Many good questions generate some degree of opinion based on expert experience, but answers to this question will tend to be almost entirely based on opinions, rather than facts, references, or specific expertise. If this question can be reworded to fit the rules in the help center, please edit the question.

  • Do you have a clip of the scene you mention? – Mixxiphoid Nov 4 '16 at 6:27
  • I've edited it with a copy of the script. – David E. Farmilant Nov 4 '16 at 6:37
  • You can quote the voice-over from the script with a > before each line if you want. Links can go dead, and having in-question quotes generally helps people understand better. – Adamant Nov 4 '16 at 6:37
  • Possible duplicate of How does Cypher exit/enter the Matrix without an operator? – Valorum Nov 4 '16 at 9:09
  • Since we know (from the Wachowskis) that Cypher entered the Matrix using an automated script, there's really no scope for him to have been in league with Trinity, nor any good reason to think that it was the case. – Valorum Nov 4 '16 at 9:26
5

I can't find anything from directors or cast which suggest this is the case. The rest of my answer is opinion, for what it's worth. Listen to that opening scene, quoted below. The script linked in the question doesn't fully match what made the final cut of the film, so I've quoted from the film itself here. Listen to the tones in their voices, which I can't type here.

CYPHER "You weren't supposed to relieve me."
TRINITY "I know but I felt like taking a shift."
CYPHER "You like him, don't you? You like watching him?"
TRINITY "Don't be ridiculous."
CYPHER "We're going to kill him. Do you understand that?"
TRINITY "Morpheus believes he is the One."
CYPHER "Do you?"
TRINITY "It doesn't matter what I believe."
CYPHER "You don't, do you?"

Cypher's words and tone tell me two things. He wasn't expecting Trinity to be there... and he doesn't want Trinity there. He believes they're going to get this person killed. They also tell me he;s already lost his faith in the mission and in Morpheus. Of course, at this point, we don't fully appreciate all that nuance, but it's there when you go back and listen.

Trinity's voice carries conviction, too. But hers is a belief in the mission, and in Morpheus. I don't think she fully believes in Neo at this point, but she believes in the search for The One.

Then... there's a pop on the line...

TRINITY "Did you hear that?
CYPHER "Hear what?"
TRINITY "Are you sure this line is clean?"
CYPHER "Yeah, 'course I'm sure."

Two things from this bit. First, this exchange would not have happened if they were in on it together. Second, listening to this, knowing what happens later in the film, listening to Cypher's tone... he was already planning something. Maybe he was going to meet with Smith, maybe just compromising a hardline, maybe only leaving a message for an agent... I don't know. But Trinity messed up his plans.

Moreover, I believe the scene where Cypher talks to Trinity over the phone while pulling the plugs of Apoc and Switch speaks for itself in this regard. Trinity is shocked and horrified by his betrayal, and even in the face of that she looks at Neo and answers "yes" to his last question. Yes, she believes Neo is the One.

So, no. Trinity was never working with Cypher.

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