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Could it be that one reason why those humans who have been freed from the matrix are stronger and faster than the humans who have not been freed be because they are less connected to the matrix as everyone else.

Before Neo was freed from the matrix he was connected to it by many plugs all over his body. After being freed however many but not all were removed by the Neb crew. When they jacked into the matrix themselves they only use one plug which I assume goes into the brain or near to it. Is this the secret to their strength within the matrix?

Second question: considering this, when Neo goes to Machine City and the machines reconnect him to the matrix using the remaining body plugs on him, since he is fully clothed how do the machines know where his remaining body plugs are?

interesting theories... and to answer...

first, i assume the plugs on the body are for life support. this is where the liquefied dead is fed through and keep the pod-borns alive since there is no point of directly pumping food into the brain. it's like spoon feeding your brain... might as well have no mouth. the plug that goes through the mouth would be the way the pod-borns breath. since they are submerged in all gooeyness, i assume they would need assistance with their breathing.

second, i don't think i saw the machines using the rest of neo's body plugs, just the one to his brain. all the other "wires" just propped him up for easy access to his head plug... it would be kinda awkward is he was standing or laying flat on the floor. even if they used the plugs in his body, the machines put them there, i think it is safe to assume that they know the exact locations of these plugs. the plugs' location are basically mathematical... they are symmetrically placed, same distance from one another... locate one, locate them all...

i also think that the p[lugs are how the machines feed (for lack of a better word) of the humans energy

If they are plugs they use on Neo (which i dont think they are) then they would go into the clothes as they are like needles

New blood.

They use those plugs at the end to zap Neo's whole body instead of just his head.

Like when someone flatlines at the hospital...they don't use the two paddles on your head....they use it on your chest.

The machines used the remaining plugs to stimulate Neo's body in real life...and to use his body as a sort of circuit breaker. They zapped Neo's body once Smith took over, and it caused Smith to get fryed.

I don't think the body plugs had anything to do with the final zapping/killing of Smith and Neo... it all happened from the neck plug port that jacked him into the Matrix