Beyond color-coding, there is a message in Mel Gibson's film -a subtext, an undercurrent, that concerns slavery. Only at the end of the world is there an end to one human throwing another into chains.
But what if the world never ends?
The final image of Apocalypto is the arrival of Europeans at the Yucatan peninsula, bringing with them a plague of smallpox and, eventually, conquistadores who would end the Maya states: one enslaving race is replaced by another, or so I would have it. The meaning is debated.
With Gibson's catholic background, expulsion from the garden is an easy metaphor. Gibson says that the final image is meant to be hopeful. I'm not sure how that can be, considering that Europeans ravaged the region for hundreds of years and enslaved the natives with as much impunity as their own had. Interpreting the arrival positively tells me that Gibson is a man divided over how to translate meaning from his own film, and that despite this being arguably his masterpiece as a filmmaker it's full impact escapes him.
Then again, that would be consistent with what we've seen of him lately, or of his actions at least: seeing him as confused and misguided is sadly far too easy these days.