The Matrix: Resurrections provided a new antagonist in the form of The Analyst, who is a far worse villain than The Architect and one of Smith's lines toward the end of the film proves it. It's not often that audiences get to see Neil Patrick Harris flex his tremendous acting chops in a villainous role, but his Analyst plays a crucial part. After the downfall of the original Matrix system in The Matrix: Revolutions, the entire system was rebuilt by The Analyst. At first, it seems like the new Matrix is pretty similar to the first in form and function. However, as time goes on, audiences are let in on just how much things have changed since The Analyst took control. More, it becomes clear that The Analyst has more sinister methods than his predecessor, The Architect (Helmut Bakaitis).
While some theories suggested Neil Patrick Harris' character is The Architect in disguise, the two are different characters with different methods of control. The Architect was made by other machines and was given a human appearance in order to try and understand human nature. His cold demeanor works well for the original The Matrix installments as the titular villain. The Architect's hatred for human chaos is palpable; he loves precision and the binary world of 1's and 0's he created as a "Utopia." While The Analyst doesn't seem like a worse villain at first, he's actually much more calculated and cruel than The Architect. Ultimately, a line provided by the upgraded Agent Smith (Jonathan Groff) proves this toward the end of the film.
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When Agent Smith saves Neo and Trinity from Resurrections' Analyst, he drily remarks, "What has the world come to? You can't even trust a program." It's meant as a deadpan joke, but it highlights just the amount The Analyst changes the Matrix. Smith felt the true power of freedom after awakening from The Architect's false, orderly reality, eventually learning to value free will and the emotion of humanity. Where The Architect dismissed human emotions as trivial, however, The Analyst uses them to manipulate and control the Matrix. This makes The Analyst not just more advantageous but also crueler than his predecessor. When Agent Smith realizes what has been robbed from him and the citizens of the Matrix, he throws this line in The Analyst's face. However, he isn't just talking about himself but The Analyst. While The Architect's method of controlling humanity was built entirely on logic and thus never personal, The Analyst presently controls humanity by making it very personal.
Whereas The Architect saw little interest in the messy parts of humanity, in The Matrix: Resurrections, The Analyst's plan capitalizes off of using human flaws and emotion against them. Agent Smith's line in Resurrections also ties back to the conversation between The Oracle and The Architect at the end of The Matrix: Revolutions. The Architect suggests that programs don't lie when discussing the truce by saying, "What do you think I am? Human?" The Analyst does, in fact, lie often and it's his lies that keep his version of the Matrix afloat. However, his own intended Utopia is so loaded with obscene manipulation that even rogue programs like Agent Smith don't want to be a part of it anymore.
