Of all The Matrix’s headscratchers, one of the biggest is why the machines don’t attack Neo when he wakes up from the Matrix - however, there are in-universe explanations for it. While The Matrix and its sequels can brag about having several iconic moments that remain to this day in the audiences’ memories, Neo waking up from the Matrix might be the most visually impactful sequence from the first movie. It encapsulates much of what The Matrix is about, and it completely flips the tone and the visuals of the film.
The question of “what is the Matrix” was the main motto of the marketing campaign leading up to The Matrix, and it created a certain level of expectations even though no one knew exactly what the movie was going to be about. Audiences all over the world wanted to find the answer to the question, and, in a way, Neo’s doubts about the world he was living in represented that on-screen. The first few minutes of The Matrix give a strong feeling that something is off, although neither Neo nor the audience cannot say for sure what it is. That changes once Morpheus enters the movie, offering Neo a chance to see what really is on the other side.
After taking the red pill and being submitted to an ominous procedure in which reality seemed to bend, Neo wakes up in the real world inside a harvesting pod located in one of the many Harvesting Fields – the place where he had lived his entire life. Neo’s sheer shock over opening his eyes for the first time did not stop him from removing the umbilical tubes and unplugging himself from the Matrix, essentially freeing himself from the machines. Although a sentinel machine did engage with Neo once he woke up, it instantly turned away once Neo was fully unplugged. That is because, from the machine’s perspective, Neo’s pod was simply defective – and its content had to be discarded. In fact, had Morpheus’ ship not been there waiting, then Neo would not have survived very long.
How Morpheus & The Nebuchadnezzar Found Neo's Body
In The Matrix, the red pill Morpheus offers to Neo serves as a symbolic, visual representation of Neo’s choice to wake up and accept harsh reality. The blue and red pills are an important part of The Matrix’s aesthetics, and their importance to the story was carried onto The Matrix Resurrections. That said, the red pill also had a practical purpose – to make sure Morpheus and the Nebuchadnezzar could locate Neo amongst millions of harvesting pods. The red pill was a tracking program, and it allowed Cypher and Apoc to pinpoint exactly where Neo’s real body was. That is how the Nebuchadnezzar managed to get to Neo so quickly after the machines discarded his body. Audiences only got to see the crew of The Matrix's Nebuchadnezzar waking up a person once, Neo, but the process was very much the same for every other human they saved.
The Matrixcan leave viewers with lots of questions, but most of them can be answered without breaking the rules of that universe. The machines not killing Neo when he wakes up is not really a plot hole, as his release from the harvest pod wasn't intended to spell his demise. However, this time, Neo’s escape would be the machine's downfall.