The film of course begins with Bruce Wayne as a neurotic young boy dealing with growing up as a child in a wealthy Gotham Family who's Paternal father figure is the President of Wayne Enterprises. Bruce's initial phobias about bats and the dark are triggered by him falling into a well where he was traumatized by bats flying around but was relieved when his father rescued him. Later in the film we see the family at the local opera where young Bruce again must see a scene where humans are imitating bats and has a phobic reaction, requesting to leave the theater early. The decision unfortunately leads to his parents death at the hands of a drug addict mugger who asks for their money but gets a little too trigger happy in the process and shoots Bruce's mom and dad dead on the spot - his father's last dying words are "don't be afraid". Bruce's development is shunted as he must deal with this horrific tragedy while trying to grow into an adult with his butler Alfred now as his primary caretaker. The film also makes it painfully clear the role that economics played in his parents death - most of the city is unemployed and broke leading to a massive crime wave and social unrest- a theme that will be ever-present throughout the entire Nolan Trilogy.
Later on Bruce plots to kill the murderer of his parents when he buys a gun and waits for him outside the courthouse but someone else whacks him first. Bruce then reveals his plot to Rachel, Bruce's childhood friend (and later romantic interest) when he reveals his gun and says to her "I'm not one of your good people", who then slaps him and tells him his father would be ashamed. Bruce then leaves Gotham to learn the ways of the criminal underworld and somehow eventually winds up in Burma in some kind of third world prison. Eventually he is rescued by Henry Ducard whom we later discover is Ra's al Ghul (Liam Neeson), the primary villain. Ducard offers to train him as a ninja and finds a way to release him from prison while leaving him vague directions of how to find his mountain temple for training high in the Himalayas. Bruce then meets him there and his training begins.
Ducard trains Bruce in the dark arts of ninjitsu. He explains to Bruce that he must learn to master and control his fear under all circumstances before he can become a true ninja warrior. He also trains him in the general tactics of stealth and guerrilla combat techniques - techniques which will come in handy later. In particular he exposes Bruce to the neuro-toxin derivative of a particular flower that causes disorientation, hallucination and confusion and tests Bruce's abilities to perform the task of hiding himself among a crowd of assassins under these conditions - a task which Bruce successfully completes though with much difficulty. Later however Bruce is introduced to the ninja master "Ra's Al Ghul" who presents him with a criminal that he is told he must execute because crime must not go un-punished. At this point he is initiated into the true intentions of the group, known as "The League of Shadows" and it is revealed to him that their plan is to burn down Gotham as it has become a cesspool of human corruption - no other path forward can be permitted. Bruce refuses to kill the criminal and suddenly realizes he is in danger - later he burns down the League's temple, killing the ninja master in the process, while saving Ducard's life before escaping.
Bruce then returns to Gotham only to find the city worse off than when he left with the powerful gangster "Falcone" practically running the town. Bruce also discovers that William Earle is attempting to takeover Wayne Enterprises which is now heavily involved in defense contracts. Bruce then meets Lucius Fox, who introduces him to the company's experimental prototype technologies, including an armored car and protective bodysuit, which Bruce takes great interest in eventually asking to be re-admitted into the corporate structure as head of R&D. Earle sees no threat in this as he believes R&D is essentially a dead-end position with little or no profit to be made where as Bruce sees it as an opportunity to explore crime fighting weaponry while secretly planning to retake the company.
Eventually Bruce begins to experiment with these technologies to the point that he is ready to embrace a new crime fighting persona - by mixing the world of ninjitsu with modern technology and overtones of bats into his outfit he becomes "Batman". As Batman, Bruce intercepts an illegal drug shipment, empowering Sgt. James Gordon and the Gotham police to arrest the previously untouchable Falcone. This act begins a partnership between Gordon and Batman with each gaining the other's trust. Gordon is thankful for Batman's willingness to put himself in harm's way to do the work the cops can't and Batman is appreciative of Gordon's honor and incorruptibility in an era of outright corruption and failure among Gotham's police force. Meanwhile, a Wayne Enterprises cargo ship is raided and an experimental weapon is stolen, a "Microwave Emitter" that uses microwaves to vaporize an enemy's water supply.
Back in Gotham, Falcone and his henchmen are declared mentally unfit for trial and about to be transferred to Arkham Asylum by the corrupt Dr. Jonathan Crane, who had been using Falcone to import a dangerous hallucinogenic drug that causes severe psychosis. Falcone, thinking he is a big shot and will be set free shortly, wishes to meet Crane's drug supplier himself - Crane refuses and further indicates that questioning his supplier would result in a request to kill Falcone. Falcone looks confused but doesn't see what's coming next - Crane puts on a dank bag over his head and blows the hallucinogenic drug into Falcone's face who immediately goes into panic and psychosis eventually saying "scarecrow" over and over and is later admitted to Arkham Asylum for the criminally insane.
While investigating Dr. Crane at his residence, Batman too is subjected to the "Scarecrow" routine and also experiences a large dose of the hallucinogenic substance - a substance eerily similar to that which he encountered high in the Himalayas albeit far more potent. He too has a psychotic breakdown and falls out of a three story building after Scarecrow lights him on fire. He is later rescued by Alfred. Not long after Rachel, who has been working with Dr. Crane to try to get his medical clearance on criminals in the justice system, is suddenly brought into a warehouse (with Dr. Crane) full of the neurotoxin which is being dumped into the water supply at which point Crane pulls a "Scarecrow" on her as well and she too goes into a psychotic state. At this point however batman arrives on the scene, disposing of Crane's gaurds and henchmen handily and eventually confronting Crane himself - he finally gives Crane a dose of his own medicine to extract information from him and watches him wig out. Watch the scene here: