[SoLiDUS]

Originally Posted by Chango

my guess is: at birth the matrix gives each individual a code that limits the abilities of everyone (IE make everyone follow the rules that the matrix has) and to make sure they accept the matrix as reality. But because of the glitch that makes 99.5% not fully accept the matrix, some people are able to do things that bend(the Crews of the hovercrafts) or break the rules (the one) so when one that can break the rules is discovered they have to reset the matrix so the code can remain intact and the matrix can continue to live

They integrate the prime code found in Neo and modify the Matrix to ensure
the present "anomaly" doesn't occur again: the illusion of choice remains ok
and they reload the system like new, or as we were told in the first movie,
circa 1999.