We see Neo flying faster than a jet when he saves Morpheus and the Keymaker in the semi collision. Neo is also probably flying a few thousand miles per hour when he catches Trinity. Wouldn't these sudden changes of direction for Morpheus, the Keymaker, and Trinity have some sort of negative affect on their health shortly after (i.e. similar to the sudden stop on the roof or a car at the end of a 50-story freefall)? One would think!
But then again, we see Jue (the female who delivers the message in Final Flight of the Osiris (The Animatrix) fall so far that when she lands, her feet send ripples through the concrete, shaking nearby dumpsters and shattering the concrete beneath her, while she is unaffected (same with Morpheus in M1 when he leaps from one building to another). It appears that sudden change of direction within the Matrix is tolerable for those who are well-trained.
Imagine a gust of wind racing down hundreds of city blocks, strong enough to pick up cars and send them into a swirling mess. How many thousands of innocent people died in this scene in order to save Trinity from landing on the car? The justification that the movie presents for this lies in remembering something that Morpheus said in the first movie about how nobody in the Matrix is "innocent":
The Matrix is a system, Neo. That system is our enemy. But when you are inside, you look around. What do you see? Business people, teachers, lawyers, carpenters. The very minds of the people we are trying to save. But until we do, these people are still part of that system, and that makes them out enemy. You have to understand, most of these people are not ready to be unplugged. And many of them are no inert, so hopelessly dependent on the system, that they will fight to protect it."
Not only that, but remember that Trinity was a big help in getting Neo to Machine City by saving Neo from Bane-Smith when she turned off the lights of the Logos, and again by piloting the Logos to Machine City when all Neo could see were machines. If Neo hadn't killed thousands to save Trinity, the entire human race would probably have died.
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