In answer to a fairly simple question on Quora – In Matrix Revolutions, what’s going on when Neo and a sentinel appear to merge? – Chris Peters (citing Philosopher Ken Wilber) wrote this wonderful explanation of what the different colour gradings mean in The Matrix universe:
The Matrix universe is themed around 5 colors, Green, Blue, Yellow, Red and White, which represent different levels of our existence.
Green is the color of the Matrix, and represents the Mind
This is the most obvious and famous color, what Wilber calls “the Green World.” Every scene that takes place inside the Matrix is tinted green. The Matrix takes place in your mind and all the challenges of the Matrix are also challenges of the mind – bending the mind to change the rules. This is why the Matrix is so appealing to us, because of the near limitless freedom it offers. In our minds, we are free to daydream almost any existence.
Blue is the “Real World” of Zion and represents the Body
You can really see the blue lighting in Zion’s dock and also in the service tunnels. Life in the Real World is harsh and unglamorous. Survival is the primary concern, death and extinction always threaten.
Yellow is the world of the Machines, representing Spirit and even Heaven
This is by far the most interesting – the Yellow World is that of Spirit. In the Matrix Universe, the Machine City is analogous to Heaven, the Architect analogous to God. A certain kind of God.
The Spirit world exists alongside the Real World. Many times in The Matrix Revolutions, we see the same shot from both perspectives – real and spirit.
Red is the symbol for corruption, evil, and Hell
In the Matrix Universe, Red is not really a world but a state of corruption and evil. The sentinels glow red from within, and the pods which hold humans trapped within the Matrix are also red.
This presents an interesting possibility with the Red and Blue pills. It might make more sense to have the blue pill free Neo, as this releases him to the blue world. However, the red pill serves this function. Perhaps this is an allusion to the (red) apple of Eden, ie, the fruit of knowledge. Often the “wrong” knowledge can corrupt us – we cannot “unlearn” something that we didn’t want to know.
White alludes to purity and the mysterious Source
Also not quite a world, the color white appears at times when Neo makes a major shift in his growth. Perhaps it represents The Source, something the films rarely explain. Certain characters wear white to suggest their purity, such as Seraph or Switch.
If you want to read the answer to the original question, you should read the full post.