The Matrix Resurrections Ending Explained
Heading into the movie's final act, and with a plan to free her from her pod in the Machine City hinging on having to choose to wake up of her own volition, Neo is visited by Lexy who asks him if he's sure this is worth risking everybody's life over. Wracked with doubt and with his head still spinning from his own release from the Matrix, he looks up at her and says the following.
"You're wondering if I'm wrong? I never believed I was "The One"... but she did. She believed in me. It's my turn to believe in her."
Given that we know that, on his own, Neo possesses no unusual abilities or code, and that it is his proximity to Trinity that seemingly activates them for him, it's not a reach to believe this might be one of the most profound and narrative-defining lines in the entire franchise. It's actually the two of them, combined, that formed The One and it was Trinity's unshakable belief in Neo - caused by The Oracle telling her that the man she loved would turn out to be The One - that provided the source of his power.
With his faith in himself gone, and Trinity not knowing anything about this mythical saviour figure anymore, it's now Neo's turn to believe in her. And he does, which imbues her with all the powers and abilities that come with being The One, saving them from the fall and allowing her to fly them both to safety.
This reshapes the entire structure of the trilogy prior to this point, and completely recontextualizes Neo's decision in his meeting with The Architect to attempt to save the woman he loved rather than "returning to the source". In a stroke, and with one line, The Matrix as a franchise ceases to be a story about the post-apocalyptic war between men and machines, or one man's Christ-like journey to save humanity, and instead one about how human connection is something that can never be quantified by calculation or study.
In our final scene, with both now believing in one another, both Trinity and Neo confront the Analyst with their entire breadth of powers and inform them they're now going to reshape the entire Matrix as they see fit. They thank him for giving them a second chance, before literally flying off into the sunset.