What?!?

why?
i thought after the trilogy..it supposed to be over!
why continue...whats goin on..storyline???
why resistance hack the matrix again...
i thought PEACE!!!
PEACE!!!
why they cont to fight?
??!?!??!

Well, the wachowski brothers thought they could make some more money, I guess.

The storyline can be found at the main site, http://thematrixonline.ubi.com/US/index.php

well the game doesn't need a real story line, the main thing i gues. is to make your character the best as good as you can

To answer your question, you keep fighting so you can expand your knowledge of the matrix, if that's even possible. But I don't think they've gone as far as they can go.