 While the game missions do run parallel to the events in the movie,  there is one mission that comes direct from the novel. As seen in  the opening moments of the movie, Bonasera the undertaker asks Don  Corleone to take action against the young men who raped his  daughter. Though its not seen in the movie, in the book, Don  Corleone has Clememzas men, including future traitor Paulie Gatto,  to "teach the boys a lesson". You get to participate in beating the  boys.