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How did he exactly obtain this connection to use some of his powers in the real world?

Every one is saying he has these abilities due to the connection with the machines but what is this connection and how did he get it?

I don't think his supernatural power is from the machine, no way, I mean, even the machine itself can't do any supernatural stuffs can it?

Well, if u buy the idea of the bible connection, that neo is actually the messiah, then wouldn't it be nice if a few miracles were carried out by him?

In revolutions, Neo went back to the oracle and asked why he was able to destroy the machines in reloaded, just by using his hands (somewhat like he stops bullets). She said that the powers of the one dont just stop in the matrix, but extend moreover. He just wasnt ready to handle the powers yet, thats why he got into that coma. But we see all that change when the story unravels