I designed this website with the same color scheme that was embedded into the Matrix movies themselves: blue/red (the current window you're reading), green (the window of links on the left), and gold (title graphics above).
Notice that everything in the Matrix is given a green tint in the movies:
The real world is given a blue tint with hints of red in various places:
Machines jacked into the Matrix from Machine City and the machine view of Machine City are gold:
Yellow takes on its traditional symbolism of fear in many scenes of the Matrix movies:
It is also worth noting that the first time Neo connects to the Source from the real world (when he destroys the sentinels with his mind), the Nebuchadnezzar is seen in the background smoldering in gold/yellow fumes, signifying not only Neo's connection to machines but also the fear everyone feels while running from the sentinels.
We know for certain that gold (Machine City) represents Heaven. There are a couple of very clear quotes to support this:
Banished from humanity, the machines sought refuge in their own promised land. They settled in the cradle of human civilization, and thus a new nation was born. A place the machines could call home, a place they could raise their descendants. They christened the nation `Zero One.' (Narrator, "The Second Renaissance, Part 1" from The Animatrix) It's unbelievable, Trin. Lights everywhere. Like the whole thing was built with light. I wish you could see what I see. (Neo, M3)
Although there are no direct quotes to support what green and blue/red represent, it is pretty clear that for humans, green (the Matrix) represents Earth, gold (Machine City) represents Heaven, and blue/red (the real world and Zion) represents Hell. If people reject the Matrix (which is created by the Architect, or God) by taking a red pill, they are flushed from the system and condemned to a life of living four kilometers below the Earth's surface and living off of "bowls of snot", as Apoc would put it.
There may be a second symbolic layer to the colors in the movies. Ken Wilber is a famous American philosopher who has published several books. The Wachowskis are fans of his work. In fact, he is the only person the Wachowskis have ever agreed to interview with in any depth about the Matrix movies.
Ken Wilber stated that gold represents spirit, green represents mind, and blue represents body in the Matrix movies. Larry Wachowski never commented on this, but the theory is interesting. In Buddhism, total enlightenment (nirvana or satori) occurs when a person connects and balances all three parts of this "trinity" (body, mind, spirit) within. Trinity provided Neo everything he needed in this regard: body (physical needs in Zion), mind (Trinity's love empowered Neo in the Matrix), and spirit (her death was needed for Neo to fully embrace his own fate of death).
As if this weren't enough for symbolism in this regard, remember that the Architect refers to Neo and all the other Ones as the "integral anomaly" since the One is a summation of anomalies. That means Trinity is Neo's "integral trinity", a phrase that is actually used to describe the "body, mind, spirit" elements of Buddhism and some other religions. What a double meaning!
All three of the movies begin with what I would call "demo" effects. If you are unfamiliar with what a "demo" is, and most people are, I recommend going to www.scene.org to download and run some of the top prize-winning demos from various demo parties. These effects have definite meaning in the movies:
There is also significant meaning in the color of clothes some programs wear. The Architect represents God and wears all white; the Merovingian represents Lucifer and wears all black; and, Seraph represents a fallen angel turned good and therefore wears black pants and a white shirt. These meanings will be supported further on the pages devoted to each character. Also, it is interesting but fairly insignificant that Switch wears both black and white inside the Matrix at different points, which probably means that her RSI "switches". Switch's costume and appearance seem to make her look like one of those people who makes you ask, "Is that a man or a woman?" It seems likely to me that Switch is confused/frustrated by her own gender identity.
There are other meanings and references when it comes to color, but this covers what I feel are the most significant elements.
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