AYes. Although it seemed that Neo destroyed Agent Smith (Hugo Weaving) at the end of The Matrix, Smith has the ability to reboot himself. In Reloaded, he returns with the additional ability of being able to replicate himself indeterminately.
AThe Architect reveals that the original version of the Matrix was designed to be a paradise free from suffering. However this version was a "monumental failure" because humans, for whom evil is in their nature and suffering is an inherent part of their life, saw through the illusion. Instead, the Architect created a version of the Matrix which resembled a somewhat dystopian version of late 20th century Earth ("the peak of your civilization"). While this version fooled 99% of people into thinking it was reality, a small number of people were ultimately unsure of it and risked rejection. As a safety valve, the machines created Zion, a supposedly free community of human beings. Zion's role was to find and remove from the Matrix human beings who could not ultimately accept its reality. However, if left unchecked, the population of Zion would eventually grow so large as to threaten the entire foundation of the Matrix and the machines' society. So the machines would gradually 'reboot' the safety valve by destroying Zion and wiping out its population. As part of this cycle they created the idea of 'The One', a being who had special ability to manipulate the Matrix. The One contained within his makeup special code which was integral to the survival of the Matrix. He was also programmed to have a generalized empathy with, and desire to preserve, humanity. With Zion destroyed by the machines, The One would be given a choice of either returning to the Matrix and guaranteeing its continued survival or of allowing the system to fail, thus killing all of the humans plugged into the system. He would also be tasked with picking a group of people from within the Matrix to create a new version of Zion, thus starting the whole cycle over again.
