He was programmed to be unkillable from the start by the architect. 

Think of it as a moment where his body was self healing and repairing and rewiring everything back to normal, to life. 

Trinity’s kiss was just a coincidence. 

That’s why Morpheus said he is the one. Not thank you trinity you saved his life. 

What would really bake your noodle is, this is what Morpheus meant when he said earlier, no Neo. I’m trying to tell you that when you’re ready, you won’t have to. 

He doesn’t need to dodge bullets, not because he can stop them or freeze them mid-air, but because he cannot die to them, or to any reason whatsoever. 

Why? 

Like Morpheus said, because he is the one. 

He is not bound by rules. 

Rules like gravity, etc. Anything. Which means he is unkillable. 

Watch the fight in Matrix Revolutions and look at how the earth shattered beneath his fall when Smith was flying while pushing his body to the ground at maximum speed. He woke up, and nothing happened to him. 

Our chosen one, unlike that of Star Wars, is unkillable, my friends. 

You think that’s air you’re breathing?