Question: Near the end of the Super Brawl, when Neo is lying on the ground helpless. Why does Agent Smith appear to act frightened and worried after he has said "Everything that has a beginning, has an end, Neo." Is it because it will mean he too has an end? And what made him say it?
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Answer: This is an echo of a line spoken to Neo by the Oracle earlier in the film. It's hard to say for certain, but I believe that given the disruption to the Matrix when Smith took over the Oracle's body, it's likely she somehow weakened him. She puts these words into Smith's head to spur Neo on - Smith is worried because he has realised what she's done.
Shay
The line was spoken to give the audience hope that Neo was coming back to win the fight. What the audience doesn't know is that Neo and the Oracle want to lose this fight, so that Smith can be destroyed. It serves as the start of a little rollercoaster of emotion, as Neo comes back, then loses, then destroys Smith. it also clarifies which Smith it is that Neo is fighting, and makes Smith not think things totally through (which helps) when he starts to copy himself into Neo (had he stopped to think for a second, he might wonder why Neo was just letting it happen).
oldbaldyone