I think it was kind of a rebirth thing, Neo was reborn as the one or something like that.
He jumped into Smith to destroy him.
__________________ "There is a time when the operation of the machine becomes so odious, makes you so sick at heart,
that you can't take part; you can't even passively take part, and you've got to
put your bodies upon the gears and upon the wheels, upon the levers, upon all the apparatus,
and you've got to make it stop. And you've got to indicate to the people who run it,
to the people who own it, that unless you're free, the machine will be prevented from working at all!" - Mario Savio
You could probably find the answer to this in every single thread on this board. Ok maybe thats exaggerated, you could find it on at least 5 just on this first page.