Zeraph

The idea was that Neo and Agent Smith were exact opposites and equals. Like two sides of an equation. Agent Smith could rewrite someone's neurons from within the matrix if they were connected to it through their neural hub, and Neo could do the same to machines.

IIRC it was an allegory for how we are becoming machines ourselves. The end was a choice, to become machine and be safe, or risk it all for human freedom and emotion? The Oracle wondering if they'd see Neo again was like saying history has a way of repeating itself.

So anyways, Neo could use his connection to the matrix to reach out and affect the machines connected to it. Kind of like a wireless router in his head...He used it to destroy the machines. In theory he could have controlled them but he was playing catch up the whole movie while Agent Smith had the advantage of being a machine and assimilating the knowledge and wisdom of other programs.

When he was destroying the drones he was pretty much doing the simplest thing he could think of, activating their self-destruct or some such (or overloading their power cell or something).

It was meant to be the real world.

Speaking of star wars...they never explain any of their weapon systems (are they lasers? plasma? None of those things act that way!) or why storm troopers wear all that armor when it doesn't protect them in the least. In fact it seems to make blaster fire worse...