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2199 is the year assumed by the Resistance to be the current date of the Real World, as Morpheus explains to Neo when he is freed from the Matrix's virtual reality, which is set in the year 1999. Morpheus tells Neo that the figure "2199" is just an approximation, because the Zion rebels aren't certain exactly what year it is.
However, the Architect later reveals to Neo that even the Zion rebels are being deceived: there have actually been six "Zions" including the current city. The only way for the Matrix program to be successfully accepted by most humans is if they are presented with the choice, albeit subconsciously, to accept the world around them as "real". This solution functioned well enough, but came at the cost that a small fraction of humans – less than 1% – would choose to reject the false reality of the Matrix (due to a questioning nature, doubts about the world, etc.). Because these malcontents might try to interfere within the Matrix, the Machines engineered the creation of Zion, as a "pressure release valve" of sorts, where humans who rejected the Matrix could be conveniently segregated. Unfortunately, over the generatons each "Zion" would grow in population until after about a century when it would start to become a threat to the Machines, at which point they would exterminate its inhabitants. A new group of humans would then be freed from the Matrix to found a new "Zion", each group thinking they were the first humans to ever escape the Matrix and unaware of previous Zions.
The result is that while Morpheus thought it was the year 2199, adding in the five previous cycles of Zions means that the current year is actually closer to 2699.