Smith is reborn in The Matrix Resurrections - here's why the Analyst kept him around. As the Wachowski sisters' original Matrix trilogy draws to a close, Smith is threatening to destroy man and machine alike, and Keanu Reeves' Neo is the only entity capable of stopping him. The One and the Machines strike a deal whereby Neo defeats Smith (sacrificing himself in the process), and Deus Ex Machina calls off the war against Zion.
Fast-forward to 2021's The Matrix Resurrections and Neo is revived alongside his also-dead lover Trinity. Both were remade by a malicious new program known as the Analyst (played by Neil Patrick Harris), who exploits their powerful connection as a foundation for a more efficient, compliant Matrix simulation. Neo is dumped into the fake world as "Thomas," a game designer, while Trinity becomes a mother and mechanic called "Tiffany." Presumably because Neo and Smith merged shortly before their mutual deaths, Neo's resurrection also results in Smith returning from the grave. You'd expect the Machines to immediately send Smith back to the recycle bin, but the Analyst has other ideas, casting the former Agent as Thomas' in-universe boss. Why would the Analyst include a program who almost destroyed everything in his redesigned Matrix?
A semi-answer is provided by Jonathan Groff's Smith shortly before clashing fists with Neo in The Matrix Resurrections' second act. Smith explains, "He [the Analyst] used our bond and turned it into a chain." The Matrix Resurrections is frustratingly vague on what this line actually means, but implies that Neo's fate is intrinsically bound to Agent Smith's. If resurrecting One accidentally resurrected the other, it stands to reason that the Analyst couldn't purge Smith without also losing his precious Neo, leaving no option but to imprison Smith within the simulation alongside Thomas Anderson. Because of his symbiotic connection to Neo, Smith would be leashed and under control - hence "used our bond and turned it into a chain." The Matrix Resurrections' Analyst kept Smith in his reboot because it was the most secure prison for a notoriously troublesome rogue program, but that plan wasn't perfect - the Analyst didn't anticipate Neo's awakening would also stir Smith's true self.
Why Agent Smith Helped Neo Defeat The Analyst
In The Matrix Resurrections' final act, Neo and his Io resistance friends launch an audacious attempt to wake up Trinity, fighting head-to-head against the Analyst at the Simulatte coffee shop. They receive some unexpected assistance from Smith, who actually shoots the Analyst into (temporary) oblivion. Why would Smith help Neo, his sworn nemesis?
On one hand, the Analyst imprisoned Smith and repressed his memories, so there's obviously bad blood between them. Smith has a great time turning the tables on his jailer in The Matrix Resurrections' final battle, but the truce with Neo can't be about revenge alone. Smith's bullets don't even kill the Analyst, after all - he's alive and well only a few scenes later. More likely, Smith would've been inconvenienced had Neo and Trinity not won their battle, so personally ensured they did.
If the Analyst had emerged victorious, he would've restored Neo and Trinity to their old places in the Anomaleum tower, buried their memories again, and restored the status quo of his Matrix universe. Smith implies ("I won't have his leash on my neck again") that Neo being imprisoned would mean the same for him, and that makes sense if Neo's awakening unleashed Smith in the first place. To retain his freedom, therefore, Smith needed to put his bitterness towards Neo aside in The Matrix Resurrections.