It was the year 1904, when Robert Angier performed his final interpretation of Alfred Borden's trick 'The Transported Man'. This trick, deemed unsolvable by magicians and impossible by the press was made only possible by the mind of Nikola Tesla, a scientist perched in Colorado Springs. It was his invention, the cloning device which Angier used to amaze audiences, and Alfred Borden's hand that killed Angier, surrounded by his prestige materials – tens upon tens of clones, dead from the minute they were born. Borden ran away with his daughter and left Angier's ingeneur Cutter Pennyworth with the materials and equipment belonging to Mr. Angier. This equipment was kept by Pennyworth, and was passed down through his family through the decades.
The Pennyworths began a new life as the servant family to the Wayne family, keeping the machine as a family heirloom in the caves under the Wayne estate. Their son Alfred, an avid reader of comic books at an early age, reads a Donald Duck comic on the topic of stealing dreams and is inspired. He becomes fascinated with dreams and at university studying engineering and dreams, but is however called to war in Vietnam. When the war is over, he begins work on shared-dreaming, but his research goes nowhere, and with no money, no employment and no prospects of a future, he is called back to Wayne Manor.
With his parents in poor health, he takes over care-taking duties for the Wayne family, but, as unfortunate as chance would have it, he falls in love with the mistress of the house – Mrs Martha Wayne. Their affair goes on behind closed doors and under the nose of the husband Thomas Wayne, completely undetected. However, Martha becomes pregnant with Alfred's child. Thomas leaves the manor for a long business trip, and in that time Martha has her child in secret. The baby is born, but quickly taken away from Martha, and the baby must leave the house before the master returns.
With no other option, Alfred uses his ancient family heirloom – Robert Angier's cloning device – to split himself in two men, each a part of Alfred's mind, but not the complete person. Alfred names the clone Miles, and sends him away with the child, who he calls Mal (a mix of the name Martha and Alfred). Miles decides to continue his dream-sharing research, and Alfred decides to stay and watch over the Waynes. They promise never to again speak to one another or acknowledge each other's existence, to protect the terrible secret of the cloning device.
The cloning device held yet one more curse – while Alfred retained all of his memories, something of the man had been lost, a drive to get away and find more, an urge for knowledge. No longer seeing the man she loved in Alfred, Martha brakes off the affair and decides to become a better wife to her husband, while retaining some form of love for Alfred. A few years pass, and Martha once again becomes pregnant with now Thomas' child – a boy called Bruce. Alfred cares greatly for Bruce, seeing him as the child he could never have had, but never getting too close to intrude, but when the ultimate tragedy strikes – the death of Bruce's parents and Alfred's former lover – Alfred takes on full guardianship of the boy. However the boy never gets over his parent's death and remains very lonely for all his schooling years. Bruce returns to Wayne Manor for one purpose and one purpose alone – to kill the man who killed his parents. Being released from what was previously a life sentence, Joe Chill is going to get out of prison to trade information about crime lord Carmine Falcone. However, Falcone kills Chill before Bruce can, and Bruce no longer knows what to do with his life. Being shown how selfish he was to only live for revenge by friend Rachel Dawes, he decides to leave Gotham City to become part of the criminal element, and learning how to fight injustice. He wouldn't return for another seven years.
Will Dormer kills Hap Eckhart in the line of duty in Alaska. He may or may be important, but he totally isn't.
Meanwhile, in another part of the world, Miles has finally invented the dream-sharing device with a small group of engineers and neuroscientists and his work is picked up by the military as a training program for soldiers – to practice fighting and the use of weaponry inside someone's mind would mean no possibility of harm, and no waste of resources – but also gains value on the black market, to be used by thieves to steal ideas and secrets out of people's minds. Dominic Cobb, the illegitimate son of a thief and con-man from London, is one of those thieves. Learning from a father who stole for fun, intrigue and the invasion of other people's privacy in any home that appealed to him as well as working for various crime lords to settle debts and helping them out with conundrums that presented themselves and who was killed by a crime lord who decided his debts were a little too high, Dominic follows in his father's footsteps until turning his head to dream-thievery. In this line of work, Dominic comes to meet the daughter of the inventor of dream-sharing – Mal. They blossom a romance and eventually even get married, with two kids, and begin to experiment with the dream mechanics, figuring out just how deep and complex the worlds they can create are.
Leonard Shelby's house is broken in by two drug addicts in which his wife is killed and he is left within a coma from a head injury. His comatose body is one of many picked by Miles as a test subject for various dream aspects. In his dream, Leonard has blended his previous life as an accountant and his story of anterograde amnesia victim Sammy Jankis with the event, creating a version of himself who believes that his wife's killer is out there and all he needs to do is hunt him down. Another person who entered the dream was John Gammell, or Teddy, who's job is to try and help Leonard to find his wife's killer, but has in told Leonard many times he's inside a dream, however Leonard chooses to forget so he still has a drive. Teddy's job mainly is to further the dream for Leonard although even he became lost within the dream as well. However, when Teddy tried to tell Leonard that he made up his own story once more, Leonard decided to shoot him, unaware he has heard the news several times and released him from the dream, leaving Leonard to continue looking for his wife's killer, but never letting himself remember what Teddy told him lest he wakes up to the horrible fact his wife is gone and no vengeance is possible.
After a long seven years, Bruce Wayne returns to Gotham, after receiving training in the Himalayas by Ra's al Ghul, who's beliefs that one must do all that is necessary to achieve justice lead Bruce to escape the order and destroy their home. When home, Bruce takes on the guise of the vigilante Batman to take down crime lord Carmine Falcone and goes on the trail of irate psychologist Jonathan Crane. He discovers that Crane is poisoning the city's water under the order of Ra's al Ghul, who wants to turn Gotham insane. However, with the help of Alfred, Lieutenant James Gordon and Lucius Fox he stops the plot and brings safety to Gotham. A year passes, and Batman's struggle against Gotham's mob is almost over as, with the help of the police and the newly voted-in District Attorney Harvey Dent. However, a new force comes to Gotham – a man known only as the Joker, with no name, other alias, identification or public record of fingerprint or blood. He spreads chaos around Gotham, blowing up hospitals and testing Gotham's citizens in sadistic ways until he kills Rachel Dawes, Bruce's oldest friend and Harvey Dent's girlfriend. Harvey, facially scarred in the attack, is convinced by the Joker that the mob killed his girlfriend. Harvey hunts down the people he thinks responsible, killing 5 people in process, and holds the new Commissioner James Gordon and his family hostage. Batman arrives and is forced to kill Harvey. With Gotham's hero being broken and turned into any other murderer you'd find in the corruption, the future of the city seems bleak, until the Batman decides to take the blame for the murders (including Harvey's), leaving Harvey to be the hero Gotham deserves. Bruce then goes into retirement, left hunted and lost within his own depression and no longer anyone's hero.
Dominic and Mal, now married and with two children James and Phillipa, are experimenting with dream-sharing techniques when they fall into limbo, unlimited dream space, where anything is possible to make. Mal became entranced by this world and didn't wish to leave, believing it to in fact be the true one. Dominic performs inception on her, to go into someone's mind and plant an idea. This idea – that Mal's world wasn't real – convinces her after what seemed like decades had passed to commit suicide with Dominic together to leave limbo. When they did, they had in fact only been asleep for a few seconds but had minds decades older than their bodies were. However, the idea that Mal's world wasn't real stuck, and she becomes convinced she was still dreaming. And so, to force Dominic to commit suicide with her, she faked a murder scene and committed suicide, framing Dom for the murder of his wife. Dominic flees the country, doing dream-thieving jobs to stay afloat in France. He is hired by Cobol Industries to steal a secret from the mind of Saito, the head of Saito Industries to repay a debt, but he fails the mission and becomes a hunted man. Saito, however, is impressed by Cobb's talent and hires him to perform inception on Robert Fischer, the son of a dying business rival, to make him split up his father's empire. Cobb assembles his team and performs the job. What Cobb doesn't know, is that Miles, who thinks of Cobb as his son, has in fact informed the whole team except Cobb of a plot to incept the idea of forgiving himself for Mal's death, while performing the job. Cobb gets over Mal's death and is, with the help of a thankful Saito allowed to land in America with ease, with Miles waiting to take him to his children.
During Wayne's self-exile, he discovers Alfred's clone Miles and questions Alfred about him. Alfred decides to show Bruce the cloning device, and reveals the full truth of his past, and all that has happened. Eight years after the death of Harvey Dent, a masked villain called Bane arrives in Gotham City, working in the sewers, building power and gaining loyalties. Bruce decides to don the Batman mantle one more time to stop Bane from completing his plan and comes across Selina Kyle, who offers to take him to Bane. At the begging of Alfred, Bruce uses the cloning machine to split himself in two, keeping one in cyrogenic freezing under Wayne Manor. Bruce goes to fight Bane but fails, and his back is broken. Gotham is sieged, under the threat of a nuclear bomb. Bruce, left in a pit to die, eventually heals his back and escapes the pit. In Gotham, Bane keeps the citizens of Gotham locked within the city and Alfred cannot reach the clone in the Batcave.
However, when Bane hears news escaping Bruce escaping the pit, he knows his full plan has been completed. There is no way Bruce could ever make it back to Gotham, and now going through all his healing just to see his city burn still would truly break him. However, Bane learns of the covert operations of the FBI and the Police Force and collects his troops to prepare for a revolution, allowing Alfred to sneak into the Manor and wake up the second Bruce. This Bruce leads an army of police officers against Bane's army of criminals, defeating him and taking the bomb out into the harbour to save Gotham. The original Bruce re-meets up with Selina and live a long life together, leaving instructions for John Blake to take on the role of the Batman, with Alfred at his side to protect Gotham once more.