The Matrix Resurrections Ending Explained

In the context of the ending, there are two key plot points in this movie. Firstly, that the key to the new Matrix is the delicate and carefully-managed combination of both Neo and Trinty. The Analyst boasts during the movie that he has set records for energy production every single year since he unlocked the key to using them both in equilibrium, and it's this greater-than-the-sum-of-their-parts analogy that defines the overall story.

Neo was seen, by both man and machine, as "The One". To his fellow humans this made him a saviour-like figure who ventured into the Machine City and brokered the peace that saved Zion, but to the machines it made him the anomaly to end all anomalies, and something that needed to be understood and quantified more than it needed to be destroyed. The cessation of hostilities that he forced them into began led them to an energy shortage that may well have destroyed them; which given the Matrix's in-universe history of how they rose to power means that fate, yet again, was not without a sense of irony.

But after decades of working through this "Neo" problem, The Analyst deuced that it was actually the combination of both he and Trinity that caused the anomaly itself. This line of dialogue in the admittedly exposition-heavy garage scene is crucial to understanding the idea.

"We worked for years trying to activate your source code. I was about to give up when I realised it was never just you. Alone neither of you is of particular value, like acids and bases you're dangerous when mixed together and every sim where you two bonded... let's just say bad things happened."

The jist here is that the code in The Matrix that enabled Neo to become The One - ie fight with incredible strength, fly around like Superman, perceive things the way the machines do, and even restart Trinity's heart - was not something inherent to him alone, but something activated by his proximity to her.

But to understand why that suddenly means Trinty can unlock those same abilities at a crucial moment, then you really, really had to be paying attention. As it's a line of dialogue that's incredibly easy to have missed...