We define the passage of time in seconds, minutes, hours, days, weeks, months, years, decades, centuries, millennia, and eons but these are all linear. The Matrix: Reloaded puts forth a strong yet creative argument for the possibility of a cyclic universe. This theme is supported not only in the movie, but also in major world religions. Christianity, for example, speaks of a newly created Jerusalem (heavenly, Zion), of a "new heaven and new earth", and a recreated universe. Other religions such as Hinduism bear this in the short-term with concepts of reincarnation and reciprocating karma. At any rate, it is impossible to deny the possibility that our universe is anything but linear.
The Matrix puts forth several intriguing parallels to the Christian re-creation viewpoint. Names of the characters alone make this poignantly clear: Neo - "new". Anderson - Germanic English gives us "man son". Zion - the heavenly recreation of Jerusalem in Christianity. The parallels to a reconstructive universe are many and varied in The Matrix, but the new movie takes this theme to an entirely new level.
On several occasions, Neo was seen to have abilities which were inexplicable or impossible in our definition of reality. His ability to "hear" Morpheus when he mutters for assistance is an unexplained yet critical indicator of his significance as a Christ-figure. The short-term theme of this characterization is thus: resurrection. The theme of a savior having the ability to give new life is also supportive of the cyclic reality theme; Neo "resurrects" Trinity after a bullet fatally pierces her heart. These examples evidence the cyclic life-span in the short term, but the movie itself failed to show this theory in the long-term until the "Architect" scene.
The point at which Neo meets the Architect is the defining moment of the proposed reality of a cyclic universe. As the movie describes, The Matrix has undergone a number of "reconstructions", six to be exact, with a mathematical remainder as an improbable anomaly.
