Then he says it: "Everything that has a beginning has an end, Neo." Smith has never called Neo anything other than Mr. Anderson before, has he? And he's repeating what the Oracle told Neo just hours before. Neo gets it - he understands the Oracle is talking through Smith, and he understands the only way to beat Smith is to let him take over and unbalance the equation. Smith and Neo are opposites created to balance an equation. And the Oracle is here to unbalance equations.
Neo allows the inevitable to happen, unbalancing the equation, thereby giving the machines control of Smith through Neo's jacked in body. Neo-Smith is destroyed by the machines, then all the other Smiths are destroyed, leaving programs he previously took over lying on asphalt, 'free' again. Smith is defeated, and the Matrix reloads to version 7, with Zion persisting this time.
Neo's body emanates white light, probably not a healthy occurrence for a flesh and blood organism, fueling speculation that his body is dead. But his mind, his consciousness, his memories...those could easily be downloaded into the machine mainframe to be born again if needed.
根据这种平衡模式，可以很好地理解剧中的人物关系。比如，先知就是为了平衡“建筑者”而存在的，所以她拥有类似“建筑者”的预知能力。NEO也不一定生来就是救世主，只是他被选中了，然后在锡安及系统的不断强化下，他的能力越来越强，最终成为 THE ONE。NEO来到锡安后，在锡安形成了不平衡，于是SMITH化身为贝恩也来到了锡安。虽然贝恩被NEO消灭了，但NEO损失了眼睛，一定程度上减轻了锡安的不平衡。
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