Released in 1999, The Matrix gained widespread acclaim worldwide. It is an iconic sci-fi film filled with great writing, world-building, fight choreography, cool special effects, and cinematography.
Keanu Reeves in a still from The Matrix (1999)
The Matrix trilogy explores the idea that everyone must choose between reality and the artificial world. While Neo represents free will, fate also plays a huge role in his journey. Undoubtedly, it has an interesting story arc with compelling action sequences, but the movie is not perfect.

The original Matrix film had its share of narrative issues and plot holes, further added by the sequels and expanded universe like The Animatrix. Some unresolved plot holes still need explanation. But here is the most confusing one.

The Matrix Plot Hole That You Realize But Can’t Unsee

When Cypher meets with Agent Smith in The Matrix
It’s already 20 years since The Matrix first amazed the theatre audiences. The Matrix is often considered a sci-fi masterpiece, but it’s not without its flaws. In the movie, one glaring issue involves a scene where Cypher meets with Agent Smith inside the Matrix to discuss his betrayal of Morpheus and Zion.

But for this meeting to happen, Cypher would have needed someone to plug him into the Matrix and then unplug him later. So, the plans of betrayal would’ve been revealed to whoever was monitoring him.

The question arises: how can Cypher execute his secret meeting with Agent Smith without anyone else knowing about his plan?

The Reason — How Cypher’s Secret Scheme in The Matrix Stayed Hidden

Who plugged Cypher in The Matrix?
Cypher is the one who usually handles the operation, so it’s possible he devised a way to enter and exit without any help — which is why he appears startled when Neo (Keanu Reeves) interrupts him.

But the speculation is not made clear here. Another doubt is how it can be executed without the order or knowledge of the captain. Maybe he was working with the machines and the agents?

No clear information explains this plothole, but Screen Rant has the answer. During a 1999 screening chat commentary of The Matrix, The Wachowskis offered some clarification for this plot hole.

According to the Wachowskis, when Neo goes to talk to Cypher while he’s on the main console, Cypher reacts by switching off his screen in a panic. The directors claim that at that time, Cypher was writing an automated code to enter and exit the Matrix on his own.

Even though it may not have been properly explained in the film — the directors’ confirmation adds credibility to this explanation for the plot hole in the movie.