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Right away from Trinity's question we learn that something, most likely bad, has happened to Neo. We know from watching Reloaded that at the end of the movie Neo some how stops the approaching sentinels and then collapses, the gang have Neo's body on board the hovercraft so we can deduce that because of taking out the machines some thing has happened to his mind, which is obviously pretty bad and complex, otherwise Trinity and Morpheus wouldn't have to go and ask the Oracle to find out what's going on. They're totally screwed. Note (from the two screen shots above) now the visual differences between the real world (typically blue) and the matrix (green and gridded) is now extremely pronounced compared with the first film, possibly symbolising the increasing separation between the worlds, or the advancement of Neo's ability inside and outside the matrix, or possibly just because Larry and the other brother that no one ever remembers the name of needed to make it more pronounced so that more people would notice it. Either way I thought I'd mention it, this is an analysis after all, isn't it? Moving on to the said clip of Neo looking like he's just had the neural interface probe stuck up the wrong hole we are obviously in for a few s