I have been a fan of the Matrix series. The most complex of the series according to me was the third part (Matrix Revolutions). I had never fully understood the movie though i had watched it many times. Heres a link where in some explanation is given about the third series. So all fans who would like to know more can visit http://cipher-quaker.blogspot.com/2007/08/matrix-re-explained.html
A long read but a good one.