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The Matrix seemingly creates a plot hole with Cypher, but there's a satisfactory explanation for the villain's actions hiding in plain sight. Although Hugo Weaving's Agent Smith takes top billing in the antagonist stakes, The Matrix reveals Cypher as a mole within Zion. Like Morpheus and the others, Cypher took the red pill and was exposed to the real world. Unlike his colleagues, Cypher deeply regrets this decision and longs to return to the blissful ignorance of digital life. To achieve this, Cypher secretly strikes a deal with Smith, selling out his friends for a free pass back into the Matrix. Cypher is ultimately killed by Tank, but not before causing considerable chaos.

However, Cypher's plan creates a perceived plot hole in the rules of The Matrix. When the people of Zion enter themselves into the Matrix, they hack in via a pirate code. This process is carried out by an operator who stays behind in the real world, while Neo, Trinity, Morpheus, or whoever it might be, is plugged in by the neck and walks the Matrix. The operator role is a vital, specialist job, and without the advanced coding knowledge required to forcibly create entrances and exits, missions simply wouldn't be possible.

Cypher's plot hole is created when the goatee aficionado begins conducting clandestine meetings with Agent Smith. Since Weaving's villain only exists inside the Matrix at this point, Cypher must meet him in the digital realm to arrange the betrayal of his teammates. But how can Cypher secretly enter the Matrix without the aid of an operator? Working by the established Matrix rules, Cypher would've needed an operator to help him jack-in and meet Agent Smith, but then, of course, the operator would've caught onto the dastardly plot against Morpheus.

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At first viewing, this certainly seems like a glitch in The Matrix. Fortunately, there is an explanation for how Cypher was able to come and go freely from the Matrix without alerting his Nebuchadnezzar crew mates. The Matrix trilogy's directors, the Wachowski sisters, participated in a (presumably very slow) chat commentary during a 1999 screening of the first movie. Discussing the mechanics of how Cypher was able to fool everyone, the Wachowskis point to a scene where Neo approaches Cypher from behind while he's working on the main console, and the villain is startled, reacting jumpily to the ninja-like Neo. The exchange seems fairly innocent at first, but after Neo emerges from the shadows, Cypher actually switches off whatever he's working on. The Wachowskis confirmed that Cypher is writing an automated code to enter and exit the Matrix during this scene.

While he may not traditionally serve as an operator, Cypher clearly has enough programming knowledge to secretly work on his own hacking sequence while everyone else is asleep. If any character other than Neo had caught him, their suspicions might've been aroused, but since Neo has only just been extracted, he's none the wiser. Knowing that Cypher wrote his own operator code sufficiently fills this particular The Matrix plot hole. Aside from coding, operators are also tasked with dropping their people into the Matrix without alerting Agents. Cypher was conspiring with the Agents, so his code perhaps didn't need to be quite so sophisticated - a simple "in and out." In the complex world of the Wachowskis, there are plenty of missing answers, but this Cypher plot hole is accounted for - even if audiences might not have noticed on their first visit.

The Matrix 4 (2021)
Release Date: Dec 22, 2021