SPOILERS AHEAD FOR THE MATRIX RESURRECTIONS
Here’s why, at the end of The Matrix Resurrections, Agent Smith saves his arch-enemies Neo and Trinity from The Analyst. The Matrix films have featured a number of notable villains, but Agent Smith, who was played by Hugo Weaving in the first three films, is without a doubt the most memorable of them all. Smith commands the agents, a group of sentient programmes tasked with ensuring the Matrix’s stability and continuity by eliminating anyone who attempts to betray its actual nature.
At the end of the first Matrix film, Neo appears to kill Smith by deleting him with The One’s powers; although he isn’t truly dead due to his connection with Neo (Keanu Reeves). However, in the Matrix sequels, this new Smith is no longer constrained by the agent programming; and instead chooses to use his newfound power and supremacy to exert his own authority and domination within the virtual world. From that point on, his major power is to duplicate himself onto other Matrix entities; resulting in the famed final showdown between Neo and an army of Smiths in The Matrix Reloaded.
While Weaving declined to return for The Matrix Resurrections, Smith did. This time he was played by Jonathan Groff from Mindhunter. This Smith still perceives Neo as an adversary, as evidenced by their lengthy fight midway through the film. Near the end of The Matrix Resurrections; Smith turns around and saves Neo and Trinity from the new adversary The Analyst (Neil Patrick Harris).
Smith saves Neo and Trinity near the end of The Matrix Resurrections for the same reason
Some may be perplexed as to why he made that decision, but it was totally motivated by self-interest; as is typical of Smith. He’d recently regained his liberty and didn’t want to lose it again. While Agent Smith was ostensibly deleted when Neo died at the end of The Matrix Revolutions; The Matrix Resurrections retconned Neo’s death, showing that the machines had reversed both his and Trinity’s apparent deaths.
Since Neo lived, so did Smith, who was suppressed by The Analyst and turned into a character in Thomas Anderson’s portion of the next Matrix incarnation. When Neo awoke from the false reality he had been trapped in, so did Smith, who felt the power that comes with freedom for the first time.
When Neo returns to the Matrix after escaping to liberate Trinity; Smith attacks him out of concern that Neo will be psychologically suppressed once more by The Analyst; resulting in Smith’s own suppression. Smith saves Neo and Trinity near the end of The Matrix Resurrections for the same reason; The Analyst was about to re-enslave Neo and Trinity, and if that happened, Smith would have lost his freedom.
Smith ensured his own existence and ability to exist; as he sees fit within the Matrix by saving Neo and Trinity. However, given Smith’s declaration that he and Neo’s odd collaboration is now gone; one may conclude that Neo and Trinity haven’t seen the last of their old foe.