Meanwhile, at 01, Neo awakens and gets up, walking towards a huge, sort of peak. There, Deus Ex Machina speaks with Neo. Neo places down his bargain about saving Zion from Smith. Deus Ex Machina asks the purpose, since all humans have tried to do is to destroy them since their birth. Neo bargains that it is the other way around, and Deus Ex Machina explains the story of the birth of the machines and how their true purpose was simply to love. Deus Ex Machina explains about evolution, and that humanity always had something the machines valued more, and that was emotion. Neo says that soon neither one of them will exist because Smith will destroy them both, as he only cares about his own selfish ways. Deus Ex Machine says that that is only because Smith is becoming human, thanks to Neo. Neo says that now he himself is becoming more machine, thanks to Smith, and that he can virtually feel them.

Back at Zion, the war is continuing and the humans are losing. As newer Sentinels and some other types of Machines dash inside and start to rip things up. The Hammer crash lands into a huge pot of squiddies, killing most of them. Morpheus and Niobi get out of the cockpit and into the lower halls, (but the Kid stays to watch), and mourn the loss of the precious Zion. Morpheus goes back to believing in Neo. Locke arrives onto the Hammer, telling Morpheus, Niobi, and The Kid to escape Zion with their lives, but Morpheus refuses, saying he will fight for his city. Niobi takes his side, saying that that "all will be lost no matter what". Locke's jealousy arises (specially since Niobi and Morph spent so much time together), and he attacks Morpheus. Morpheus and Locke fight for a while, and Morph gets the upper hand. Niobi tries to break it up, but there is no such thing. Locke grabs the electro-gun and shoots at Morpheus, knocking him for a whirl. Locke screams at Morph about his foolish beliefs in Neo and the prophecy of the One, and such, calling him names. Niobi has had enough, revealing she loves Morph, and grabs the gun and blasts Locke three times, killing him. Morph and Niobi have a short conversation about love, and they embrace.

Deus Ex Machina drops the revelation that all of those born into bondage have that ability, due to the fact that all humans are relatively part machines. Neo is shocked to learn this, and Deus Ex Machina explains that the purpose of the One is to help the machines themselves discover love. He says that there is no truth without lies and that they needed to fool the humans into believing several things (the skies, the One, that they are fully human, that Zion can survive), and its all a part of control to become human, which was the Machines true purpose, shocking as it is. Neo partially believes Deus Ex Machina, due to the fact that he can sense truth due to his machine senses. Deus Ex says that now that Neo has been the first human/machine anomaly to feel the emotion of love, they need him to touch the source (implanting the code of emotion and love to all machines) and end the struggle once and for all. Neo thinks harshly, realizing that if he had touched the Source, that perhaps the war could be over, but Neo also realizes that he can't fully trust Deus Ex. Neo strikes a bargain, saying that if he Deus Ex Machina spares Zion and his people, as well as bringing Trinity back, that he will rid the Matrix of Smith and touch the Source for them.

Deus Ex, skeptical at first, agrees and Neo is jacked in.

The signal from 01 of the Matrix is sent into Zion. All of the Sentinels stop their attack suddenly, and all of the humans watch the Matrix on the monitor, preparing for the Superbrawl...