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The second Matrix movie.
Neo wakes up from a nightmare of Trinity being killed by the Agents. Morpheus receives a message from Captain Niobe, his former love interest, about Osiris' message that the machines are having a city and planning to use a drilling device to go to Zion. While in the meeting, Neo is given an Agent's earpiece and gets into a fight with 3 Upgraded Agents. He wins against them and flies away to meet the Oracle, but she is not here.
In Zion, Morpheus has announced the news of the machines' plan. Neo goes into the Matrix to find out that the Oracle is a program, so is her bodyguard, Seraph. When asking how he can trust her, the Oracle replies that it is his decision. Neo encounters Smith, but this time, he is not acting like an Agent. It is revealed that after being destroyed by Neo, he is supposed to go to the Source, but due to getting a part of Neo, he becomes a rebel like. He demonstrates that he clones himself by using people as hosts. Neo tries to win, but too many Smiths causes him to flee.
Afterwards, Neo, Trinity, and Morpheus meet the Merovingian, who refuses to give the Keymaker to them. However, his wife, Persephone betrays him and led the them to the Keymaker. Neo gets into a fight with the Merovingian's henchmen and ended up in a mountain. Meanwhile, Trinity and Morpheus deal with the Twins and Agents. Neo has rescued both Morpheus and the Keymaker.
The group, along with Vigilant and Logos, plan to help Neo get to the Source. Trinity goes to the Matrix and gets into a fight with an Agent. Meanwhile, Neo, Morpheus, and the Keymaker confront Smith, but they escape with the Keymaker being killed.
In the Source, Neo meets with the Architect, the creator of the Matrix. He is given a decision: go to the source or back to the Matrix to save Trinity. Neo chooses the second option. He saves Trinity from dying by removing the bullet and reviving her.
In the real world, the Nebuchadnezzar is shot down and the group are forced to walk. Neo has managed to stop the Sentinels by his power, but fainted. Another man is with Neo: Smith possessing Bane.