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At the end of the previous film / Neo (Keanu Reeves) finally realized his abilities and mission. After being shot and resurrected / he became an omnipotent "savior." He and his girlfriend Trinity (Kelly-Anne Moss) and captain Morpheus (Laurence Fishburne) returned to Zion / the human base / and were warmly welcomed by people. At this time / the "Matrix" decided to strike first and sent 25 / 000 electronic squids to attack the Zion base; Morpheus / Neo and Trinity entered the "Matrix" again / looking for the "Key Maker" and preparing to destroy it from the inside; and Special Agent Smith / who was supposed to be eliminated by Neo / seemed to have something wrong / broke away from the control of the "Matrix" / and possessed terrifying copying abilities / hindering Neo's actions.
上一部结尾，尼奥（基奴李维斯 饰）终于意识到自己的能力和使命，中弹复活后，变成了无所不能的“救世主”，他和女友崔妮蒂（凯莉·安·摩丝 饰），舰长墨菲斯（劳伦斯·菲什伯恩 饰）回到了人类的基地锡安，受到人们的热烈欢迎。 此时，“母体”决定先下手为强，派出了两万五千只电子乌贼攻击锡安基地；墨菲斯、尼奥和崔妮蒂则再次进入“母体”，寻找“制钥者”，准备从内部破坏；而本该被尼奥消灭的特勤史密斯似乎出了点问题
