The guy who tried to kill Neo and the traitor on the stretcher were the same man, and I think he appeared once earlier in the film as well. When the team retrieved the message from The Oracle, one of them took the message and rang out of the matrix first. The other faced Agent Smith and was infected by him, virus-like. He then also rang out of the matrix into the real world. I think that the man taken over by Agent Smith was the same man who later tried to kill Neo, tried to get his ship volunteered to go with Neo's, and ended up betraying the presence of the fleet to the sentinels. And I think that he made it into the real world with Agent Smith still inside the body. Obviously this calls into question the very nature of reality as we've understood it up to this point. And yes, I'm aware that immediately after the scene in which Agent Smith appears to ring into the real world, Neo wakes up. But all of Neo's other dreams come true, and this one certainly did as well, as evidenced by the subsequent delivery of the message from The Oracle that the first man had been carrying.
If in fact I'm correct, and Agent Smith made it into the real world, that also explains how Neo was able to stop the sentinels. Perhaps because of the connection to Agent Smith that the Agent mentioned earlier in the film, perhaps because of the dream, perhaps because of something The Architect said, he suddenly found himself with some subconscious understanding that he wasn't really outside of the matrix at all. That he had some awareness of things happening in the real world much like he does inside the matrix. He was able to control the sentinels because the sentinels exist within the uber-matrix, which is what I've decided to call the new reality. However, seeing the confirmation of his unreality in the form of the sentinels dropping dead to the ground put Neo into a coma. After all, he's too old, remember? What exactly happens when people whose minds are rigidly set one way suddenly encounter a reality they can't accept? I suspect that they go into the sort of coma Neo is in right now.
And now for my really wild theory. I wrote this theory section on Friday night, adding this entire introduction Monday morning.
My Wild Theory
At the end of Reloaded, we learn that Neo can both sense the sentinels and exercise some measure of control over them. The act of terminating the three sentinels sends Neo into an apparent coma. Could this be what happens when someone is too old and set in his days suddenly encounters the realization that he has been living inside the matrix? We were told in the first film that normally people are taken when they are young to avoid problems, perhaps like this one. Neo could have realized, seems to have realized, that he is not really in the real world at all, as we would recognize it, but instead still within an "uber-matrix." That would explain also the earlier scene in which an Agent Smith-infected "human" is sucked out of the matrix into the "real world." Yes, it was a dream, but Neo's dreams come true. Always. That was the agent that fell into the car, the first dream was accurate. Or there might be an alternate possibility that I'll address later.
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1 - Phillip Winn
MATRIX RELOADED SPOILER: I meant to mention, but then forgot, the interesting possibility that Neo did not actually stop those sentinels after all. In fact, this was the first thing I said after exiting the theater - Did Neo actually stop those sentinels, or did the ship coming over the hill set off an EMP at just the right time? Shades of A Case Of Conscience float through my mind.