Evil Dead
Enemy of the Gospel
I'll try to answer these in order:
1. Your mind can enter the Matrix because the Matrix is simply computer code that is transmitted through the ports in the person's body into electrical impulses......electrical impulses are the signals sent to our brain which controls the way we percieve reality. This allows the electrical impulses sent into the brain from the Matrix to fool the brain into thinking they are naturally occuring electrical impluses that we use everyday to see, hear, feel, etc.
This cannot be done in reverse as the human body has no program inside of it to decode a computer program and transform it into electrical impulses. The Smith program could not invade a human's body because the human body does not have software to read the code....a computer program is needed to decypher the code (like the Matrix.....it decyphers the code when a person is jacked into it).
I'm sure you've all played ROMs on your computer with an emulator......why won't roms work without an emulator?.....the code is there for the game....so why won't it just play? It won't because you need the program installed on your computer that decyphers this code...this program is called an emulator.
An easy analogy: Smith is a Rom.......the Matrix is an emulator.....Smith can exist in the Matrix because it decyphers the code for his program. He however can not exist in a real world because the human body does not have an emulator program to decypher his code...it has no programs at all......it has only a brain and nerves in which information travels throughout the body.
2. We still don't know if Neo actually stopped the Sentinals......it could have been the aproaching ships e.m.p. ................if he did, it is just as plausable that he realized that he was still inside of a computer program and used his powers to stop the sentinals as your explanation was.
3. Why do the agents want the codes for Zion in the first movie? Because that is their program.......in the Reloaded the architect tells us that Zion must be destroyed as it has the previous 5 times.......the agents are programmed to try to get the codes so this can happen......
or
The agents only function (as seen in the movies and the Animatrix shorts) is to stop people from waking up and realizing they are in a program (think of the Animatrix short "world record"😉........if they destroy Zion, there will be no more rebels hacking into the Matrix to free people's minds. There job will have been done................what makes you think that an agent program would even know that Zion was another program in the first place? Wouldn't they be more efficient if they thought Zion was real........that there was a real threat?.....programs only know what their function is.......they do not know what other programs in the same system's function is.............my solitaire program on my computer has no clue what the function of my Adobe photoshop program is...........if solitaire was programmed to try to stop me from opening Adobe Photoshop, it would try to do just that. Every program in the Matrix is a piece of a puzzle..........none know what the other's function's are (and they all have one as the Oracle says, "nothing is coincidence....everything serves a purpose"😉 the only ones who can put the puzzle together are the audience.......we can because we see each program functioning and can realize their purposes........I'm sure the agents don't even know what Persephone's or the Oracle's functions are inside of the Matrix, but we do.