This is just a take on the thought of what if Smith won, what next? This is obviously an AU. Sorry if this offends anyone. I don't own the concept of the Matrix, just as well, if I had it wouldn't be quite the same story and I like it just the way it is.
Ch 1 Another Ending
Smith pulled back from Neo, he had him just where he wanted him, but something just didn't feel right. A trap, he still remembered how it felt when Neo had invaded him and cast him from his original purpose. Smith stepped back and watched his nemesis as he lay broken on the ground.
Neo shook his head "why?"
"Why what, Mr. Anderson?" he said in his even tones.
"Why didn't you take me, you've won" he said, staring up at Smith.
"Yes I've won, I don't need you" Smith said. Carefully.
Neo shook his head again and vanished, back to his body. Smith knew he wouldn't last long. Smith felt for his other selves and felt their search, it was only a matter of time.
Deep within the Matrix a Smith stirred, something was wrong. He didn't feel right. He kept these feelings to himself. He knew himself well enough to know any change would be dealt with instantly and he wished to continue his existence. And so the first stirring of change started. After all, nothing ever stays the same.
AN: There are going to be several Smiths, I guess I'm going to have to figure out some way to identify individuals. This is something I haven't had to deal with before, Oh well, I'll figure something out. Sorry this is short, I'm just setting this up.