Note: this does contain some spoilers. If you haven't seen the film, then don't read this.

There's always been fan fiction stories here and there of this and that.

But for this movie it'd be interesting.

In general I never looked at this as good guy vs bad guy more like democrats vs republicans. Neither side seems good nor bad.

But an idea for a fan fiction would be this.

Neo takes the blue pill instead of the red pill. The next day he then goes to the agents building and apologizes for being rude and puts a counter offer on the table saying he'all help them if they don't bug him and also teach him how to do the mouth thing.

Agent smith then cordially evilly smiles agreeing and says he'll teach Neo to do even more stuff like that.

Neo then even agrees that Morpheus is dangerous as he given gave him drugs.

Agent Smith tells Neo that they have an inside guy Cypher.

And basically Neo and the agents win after some fought out battles.