Neo is a plain human in the real world in M1. Nothing peculiar there. And just like every other human, who plugs into the Matrix, it’s just his mind that’s transformed into a residual self-image. This RSI is a PROGRAM.
In M1 Neo assimilates a special program into his RSI-program. Namely the anomaly-code.
When his mind is down-loaded back into his human body, so is the anomaly. Think of it like remembering a dream. You haven’t really BEEN where you dreamt you were, or done what you dreamt you were doing. But the memory is still there. Just like the anomaly.
Ahnold> The anomaly code doesn’t vanish when Neo’s mind is downloaded back into his body. It goes right in there with the mind.
What are thoughts really? Electro-chemical signals. So the digital anomaly code is transformed into electro-chemical signals along with the rest of his mind.
Until Reloaded Neo isn’t aware of this. As Hammann says when he talks to Neo in engineering: “I have no idea how you’re able to do some of the things you do. I just hope we’re able to figure it out before it’s too late.” Hammann has such a good point, that everyone forgets in the “oh, woaw” when Neo kung-fu’s three agents to shish-kebab. HOW does he do it? And WHY can he do it? (Even when the Mero asks about “why”, no one asks about Neo’s power).
The anomaly-code is active both inside and outside the Matrix, as it is connected directly to the Source.
I hate to say that but "Neo can stop sentinels in the real world 'cause he is connected to the source" the most superficial an annoying answer to the question. How can he stop things in real world? The answer is: I don't know!!!...And I guess even the Super Wacho Mario Bros don't know too. Is another open question left by the Wachowskis to start discussions in forums like this...I loved RVL but the Oracle's explanation about Neo's power in the the real world was a deception.... 🙁