Why did the analyst leave Agent Smith in his reboot of The Matrix

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Smith is reborn in “Resurrections of the Matrix” — that’s why the Analyst kept him around. As the Wachowski sisters’ original trilogy, The Matrix, comes to an end, Smith threatens to destroy both man and machine, and Keanu Reeves’ Neo is the only entity capable of stopping him. The Former and the Machines make a deal whereby Neo defeats Smith (sacrificing himself) and Deus Ex Machina cancels the war against Zion.

Fast forward to the “Resurrections of the Matrix” in 2021, and Neo will be reborn together with his also dead beloved Trinity. Both have been remade by a new malware known as The Analyst (played by Neil Patrick Harris), which uses their powerful connection as the basis for more efficient Matrix modeling. Neo enters the fake world as “Thomas”, a game designer, and Trinity becomes a mother and mechanic named “Tiffany”. Presumably, since Neo and Smith merged shortly before their mutual death, Neo’s resurrection also leads to Smith’s return from the grave. You expect the Machines to immediately send Smith back to the trash, but the Analyst has other ideas and makes the former Agent Thomas’ boss in the universe. Why would an Analyst include a program that has destroyed almost everything in its redesigned Matrix?

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A half-answer is given by Smith from Jonathan Groff shortly before the clash of fists with Neo in the second act of The Matrix: Resurrections. Smith explains, “He [the Analyst] used our connection and turned it into a chain.” Matrix Resurrections is frustratingly vague about what this line actually means, but the implication is that Neo’s fate is inextricably linked to Agent Smith’s. If the resurrection of One accidentally resurrected the other, it goes without saying that the Analyst could not purify Smith without losing his precious Neo, leaving no choice but to imprison Smith in the simulation along with Thomas Anderson. Because of his symbiotic bond with Neo, Smith will be on a leash and under control-hence, “used our bond and turned it into a chain.” The Matrix Resurrections analyst left Smith in his reboot because it was the safest prison for the infamous rogue program, but this plan wasn’t perfect-the analyst didn’t expect that Neo’s awakening would also affect Smith’s true self.

Why Agent Smith Helped Neo defeat the Analyst

In the final act of The Matrix: Resurrections, Neo and his friends from the Io Resistance make a daring attempt to wake up Trinity by fighting face-to-face with an Analyst in the Simulatte coffee shop. They receive unexpected help from Smith, who actually sends the Analyst into (temporary) oblivion. Why would Smith help Neo, his sworn enemy?

On the one hand, the Analyst imprisoned Smith and suppressed his memories, so there is clearly enmity between them. Smith has a great time turning tables with his jailer in the final battle of The Matrix: Resurrection, but a truce with Neo can’t just be about revenge. After all, Smith’s bullets don’t even kill the Analyst-he’s alive and well just a few scenes later. Most likely, Smith would have been uncomfortable if Neo and Trinity hadn’t won their battle, so he personally made sure that they did.

If the Analyst came out victorious, he would return Neo and Trinity to their former places in the tower of the Anomaleum, bury their memories again and restore the status quo of his Matrix universe. Smith hints (“I don’t want his leash around my neck anymore”) that Neo’s incarceration will mean the same thing to him, and it makes sense if Neo’s awakening provoked Smith. Therefore, in order to preserve his freedom, Smith had to put aside his bitterness towards Neo in “Matrix Resurrections”.