Batman Begins Beats

ACT 1

Opening Image: In this initial scene of the movie, you learn who Bruce and Rachel are as they play around the yard as young children. From this scene you can notice that Bruce was born into a very wealthy family. It soon flashes to a more recent time period where Bruce spends his time out on the streets, seeming to fight evil. Around this point in time is also when we first meet Ra's Al Ghul.
Theme: "Become more than just a vigilante." The theme behind Batman Begins is for Bruce to make a legend of himself.
Setup: The first setup of the movie takes place during the childhood flashback where Bruce is terrified of bats. Within a few moments, there is another setup where Bruce gives back the arrowhead he stole from Rachel. Later Bruce gives a coat to a homeless man who states "This is a nice coat." Further along in the movie there are more setups where Rachel tells Bruce "It's what you do that defines you.", "Didn't you get the memo?", and "Our company's future is secure."
Catalyst: At this point in the movie, Bruce has just asked his parents if they could leave the opera early and when they walk out of the theater they are immediately greeted by a man trying to mug the family. Despite throwing his wallet on the ground, the mugger shoots both Bruce's father and mother, leaving them dead as he runs off. At this point, Bruce's life is changed forever.
Debate: The initial debate takes place when the man who killed Bruce's parents is going back to court for the possibility of being granted parole. Bruce does not agree with this and wants to take revenge against the man who killed his parents by keeping a gun in his jacket so that he can shoot the mugger as he leaves the courtroom. However, this does not take place because upon walking up to the mugger, someone else suddenly shoots and kills the mugger. This causes Bruce to leave the court area and drive downtown where the town's mobster takes residence. Before going in to the building, however, Bruce realizes that he could never kill anyone (this is also a setup for later in the film as Bruce is training) and he throws his gun into the water before going into the mobster's shop. While Bruce does get beaten up a little bit, he also tells Falcone that he is not afraid of him.
Break Into Two: Bruce leaves Gotham for years, catching up with what was going on during the opening image where he meets Ra's Al Ghul and Ducard and begins training with them to potentially become part of the League of Shadows. However, at one point they ask for Bruce to execute a man(this is the payoff we set up for by throwing the gun in the water earlier), and Bruce states that he can not do it, instead he lights the building on fire and gets himself and Ducard out. Bruce brings Ducard back to his burnt down house and makes the decision to leave and return home to Gotham. 

ACT 2

B-Story: During the B-Story we initially meet  and allow for some character development of Dr. Crane, Gordon, and Fox. This is also the point in time where Bruce "comes back from the dead." 
Fun & Games: Bruce makes his way back to Wayne Enterprises and decides to go snooping in the Applied Sciences department. Bruce works together with Fox to get together all of the different equipment necessary to build the Bat Cave, Batman Suit, and even the Bat mobile.
Midpoint:After playing around with his new toys, Batman makes his first real impression by taking down Falcone and leaving him chained up to a light in the shape of a bat. (This is a setup for the later creation of the Bat Signal in the next movies.) 
All Is Lost: Ducard comes back explaining that he is trying to purge the city of Gotham and sets the Wayne Manor on fire, after Scarecrow is blasted by his own fear gas, all of the other prisoners are set free, and finally a large log falls on top of Bruce, making it seem as though this is how Bruce is going to die.  
Dark Night of the Soul: "I wanted to save Gotham, I failed."
Break Into 3: Batman makes the decision that he is going to go and fight the gas and Ducard.

ACT 3

Finale: Batman fights Ducard on the monorail and when it appears the the monorail is going to make it to the Wayne Enterprises and release the gas throughout the entire city, Gordan suddenly clears the path by causing the monorail track to break and fall apart as he is driving the Bat mobile. Ducard is left on the train to fall off the tracks and die as Batman gets out and gets away. Fox is placed back on the board at Wayne enterprises, firing Earle and taking his job. Bruce goes back to his home where he kisses Rachel and they walk of smiling. 
Final Image: Various people are walking around looking at the ruins of the Wayne Manor and Bruce states that he intends to rebuild the manor just as it was before.

Deus ex Machine Moment
During Batman Begins the  Deus ex Machina moment took place when Gordan drove the Bat mobile, breaking the monorail so that it would fall off the tracks before reaching Wayne Enterprises and releasing the fear gas throughout the city. 

Favorite Setups
One of my favorite setups was when Bruce gave his coat to the homeless man so that later in the movie it could be payed off by Batman when he sees the homeless man while fighting and states, "Nice coat." providing some comic relief before taking off again to finish fighting off the bad guys.

The way Rachel found out who Batman really is was also a good setup/payoff. Earlier in the movie Rachel was talking to Bruce about how, "It's what you do that defines you." So when Rachel tries to figure out who Batman really is, he just has to repeat that line and suddenly Rachel was able to realize who he really is.