The Matrix is one of my favorite movies of all time. For about 5 years between 1999 and 2004, I was completely obsessed with it. Then on approximately my ten thousandth viewing, I noticed something new and its irrevocably damaged my enjoyment of the film.
In the middle of the movie, there is a scene at a steakhouse where Cypher meets with Smith and agrees to betray the crew of the Nebuchadnezzar in return for re-insertion to the matrix. Cypher posits an interesting philosophical question, "If you could chose between a simulated reality indistinguishable from the real thing in an generally pleasant world or live in a truly real but miserable reality, which would you choose?" Cypher gives his answer with a big bite of steak and chooses re-insertion. It's too bad that this scene could have never happened...
The scene takes place in the matrix. It is established during Neo's training sequence that the matrix is a dangerous place for the unplugged. Agents can emerge from nowhere, have super powers which exceed their own, and are programed to kill them. This is not the kind of place you go into alone. Furthermore, it is established in this movie and its sequels that there must be an operator on the outside to put them in and take them out. It is also the operator's job to monitor the others while they are inside. There also seems to be a regular watch on the matrix even if no one from the Nebuchadnezzar is inside. Are you starting to see the problem? There is no way that Cypher could have gotten the privacy he needed.
The steakhouse scene takes place in complete isolation. There is no clear indication of how he got in or out or who was watching him as he sat plugged into the matrix in the middle of the ship. Even if he found a way to get himself in and out on his own or broke away on a regular mission, there is a big green glowing monitor on the outside showing him having a pleasant conversation with the enemy. That's usually the kind of thing that gets the commander's attention. And from the context of the conversation at the steakhouse, it is clearly not the first time he's spoken to an agent.
The scene only makes sense if Cypher has a co-conspirator on board. Tank or Dozer are the most likely candidates as they are the designated operators and are on the outside when Cypher makes his move, but being born in Zion (no plugs), they have the least to gain by working with the machines. I doubt they can be put in the matrix at their age. Furthermore, they don't do anything to help Cypher with the killing their friends thing even though they are in an excellent position to do so and they seem genuinely surprised when Cypher starts shooting them with that lighting gun. (Who wouldn't be?)
Maybe it was one of the other unplugged crew members. After all, they've seen both realities. One of them may have made the same choice that Cypher did. The conspiracy may have started as some idle banter about how much they miss Chinese food. So, who is it? I think it's safe to assume it's not Trinity, Morpheus or Neo. Mouse is done by agents while Cypher is allowed to escape the matrix and proceeds to kill Apoc and Switch.
The movie never acknowledges a co-conspirator in any way leaving the steakhouse scene as a logical inconsistency. Now my feeling of this scene is the same as Cypher's, "Ignorance is bliss."
P.S.- I don't think I can discuss The Matrix without acknowledging the sequels. I won't attempt to defend Revolutions, but Reloaded deserves much less hatred than it gets. From the first appearance of the Merovingian to the end of the car chase, there is a solid hour of excellent action including the every weapon fight and the Rasta Twins. The conversation with The Architect is also one of the most interesting bits of philosophy in the series.
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