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，脱离了“母体”的控制，拥有可怕的复制能力，阻碍尼奥他们的行动。Six months after the events depicted in The Matrix, Neo has proved to be a good omen for the free humans, as more and more humans are being freed from the matrix and brought to Zion, the one and only stronghold of the Resistance. Neo himself has discovered his superpowers including super speed, ability to see the codes of the things inside the matrix, and a certain degree of precognition. But a nasty piece of news hits the human resistance: 250,000 machine sentinels are digging to Zion and would reach them in 72 hours. As Zion prepares for the ultimate war, Neo, Morpheus and Trinity are advised by the Oracle to find the Keymaker who would help them reach the Source. Meanwhile Neo's recurrent dreams depicting Trinity's death have got him worried and as if it was not enough, Agent Smith has somehow escaped deletion, has become more powerful than before and has chosen Neo as his next target.