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Spoiler
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Thought about it just being another matrix, and it seems like quite a likely plot twist/ending to me. The best point made here is probably #2 by Secret . She can either be a rouge program that's travelled through (I guess this is right) two matrices (hehe), or she could just be what she said in this movie, that she's just doing the job that she was designed to do - fortell the future (all she really did was allude to this, but hey, I'm taking a bit of license).
I'm thinking Agent Smith is basically the same as he always was, except that now he isn't controlled by whatever higher power in the machines is fueling this. Seems to me he's doing the same stuff he was the first time around, except that now he can alter people's minds so that they mentally become him. On this, though, what happens to these clones? Should we expect in the third one to see an army of a billion of them walking the earth in search of Neo (similar to The Langoliers)? Just a thought, since all we see them do is walk out after fight scenes.
As for Neo's powers to stop the sentinels, I have to hope that he's in another matrix, otherwise, like OMFUG said, this would be a really sad cop-out.
I was thinking a good ending would be for the movie to just suddenly twink out to a white dot on a tv screen, and to have someone come by and turn it off. Just trying to think of something highly unlikely, since I've found that's really the only way to predict what's going to happen in this movie series (i.e. when Merovingian's wife moves to the two open doors to shut them, I thought, "What's the coolest thing they could do with this? Have them lead somewhere else," and they did. I give myself no credit here, however, just a lucky guess).
OK, one more point before I give my fingers a rest, what exactly was The Architect talking about with the last set of choices that Neo has to make? I completely understand the decision that they've set in front of him, but why would they do that to begin with? Why give the humans however many people he said and give them a chance to rebuild? Maybe that would give the machines purpose, I don't know. That didn't make much sense to me, but I guess the point is moot now anyway, seeing as how he didn't take that one.
After all this, I'm thinking the most probable story line would be that it's all another matrix. That's the only concievable way that Neo could sense anything different when he's not plugged in.
That's all I've got. Whew.
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