In 1995, John Connor is ten years old and living in Los Angeles with foster parents. His mother Sarah Connor had been preparing him throughout his childhood for his future role as the leader of the Human Resistance against Skynet, but was arrested after attempting to bomb a computer factory and imprisoned at a mental hospital under the supervision of Dr. Silberman. Skynet sends a new Terminator, designated as T-1000, back in time to kill John. The T-1000 is an advanced prototype composed of a mimetic polyalloy that allows it to take on the shape and appearance of almost anything it touches, and transform parts of its anatomy into knives and other stabbing weapons. The T-1000 arrives under a freeway, kills a policeman and assumes his identity. Meanwhile, the future John Connor has sent back a reprogrammed T-800 (Model 101) Terminator to protect his younger self.
As a child, Bruce Wayne falls down a dry well, where he is attacked by a swarm of bats; he subsequently develops chiroptophobia. While watching an opera with his parents, Bruce is frightened by performers masquerading as bats, and asks to leave. Outside, the family is targeted by a mugger, Joe Chill, who murders Bruce's parents, leaving him to be raised by the family butler, Alfred Pennyworth.
In the winter of 1929, Nick Carraway, a Yale University graduate and World War I veteran, is staying at a psychiatric hospital to treat his alcoholism. He talks about Jay Gatsby, describing him as the most hopeful man he had ever met. When he struggles to articulate his thoughts, his doctor, Walter Perkins, suggests writing them down, since writing is Nick's true passion.
In Gotham City, Batman stops a hostage situation in a bank caused by Two-Face, the alter ego of the disfigured former district attorney, Harvey Dent. However, Two-Face escapes. Edward Nygma, a researcher at Wayne Enterprises, develops a device to beam television directly to a person's brain; Bruce Wayne—with whom Nygma is obsessed—rejects the invention, noting that it "raises too many questions", and Nygma angrily resigns from his position after killing his supervisor Fred Stickley, and forging his suicide note and footage. Everybody except Bruce is convinced it was a genuine suicide. During a news report, it shows how Harvey Dent became Two-Face: While he was prosecuting Sal Maroni, Maroni threw acid in Harvey's face; Batman tried to stop him but failed. After meeting Batman-obsessed psychiatrist Dr. Chase Meridian, Bruce invites her to a charity circus event. There, Two-Face and his henchmen storm the event in an attempt to discover Batman's secret identity, and in the process murder The Flying Graysons, a family of acrobats who attempt to stop him. The youngest member, Dick, survives and throws Two-Face's bomb into the river to detonate safely underwater but the rest of the family dies.
In 1954, two U.S. Marshals - Edward "Teddy" Daniels and his new partner, Chuck Aule - travel to the Ashecliffe Hospital for the criminally insane on Shutter Island located in Boston Harbor as part of an investigation into the disappearance of patient Rachel Solando, incarcerated for drowning her three children. The sole clue is a note left by Solando, which reads: "The law of 4; who is 67?" Shortly after arrival, a storm prevents their return to the mainland for several days. Daniels finds the staff confrontational: the lead psychiatrist, Dr. John Cawley, refuses to hand over records of the hospital staff; Solando's doctor, Dr. Lester Sheehan, had left on vacation after her disappearance, and they are barred from searching Ward C and told that the lighthouse on the island has already been searched, so there is no need to search it. When a patient is being interrogated by Daniels, with a subterfuge she sends Aule away for a few seconds and scribbles "RUN" in Daniels' notepad.
Batman and Robin fail to stop Mr. Freeze from stealing a cache of diamonds. They learn that Freeze was once a scientist named Victor Fries, who became dependent on a diamond-powered subzero suit following an accident in a cryogenics lab while working to save his wife, Nora, from a terminal illness called MacGregor's Syndrome.
After eight months of treatment for bipolar disorder, Pat Solitano is released from a mental health facility in Baltimore, and returns to Lansdowne, Pennsylvania into the care of his father Patrizio and mother Dolores. Pat soon learns that his estranged wife, Nikki, has moved away, and that his father is out of work and resorting to illegal bookmaking to earn money with the hopes of opening a restaurant. Pat is determined to get his life back on track and reconcile with Nikki, who obtained a restraining order against him after a violent episode sent him away.
A deadly virus wipes out almost all of humanity in 1996, forcing remaining survivors to live underground. In 2027, James Cole (Willis) is a prisoner living in a subterranean shelter beneath the streets of Philadelphia. Cole is selected for a mission, where he is trained and sent back in time to collect information on the virus in order to help scientists develop a cure. Meanwhile, Cole is troubled by recurring dreams involving a foot chase and an airport shooting.
Psychiatrist Dr. Miranda Grey (Halle Berry) works at a mental hospital and has a car accident after trying to avoid a girl (Kathleen Mackey) on a road during a stormy night while driving back home. She rushes to try to help the girl. The girl turns out to be a ghost and possesses Miranda's body by burning her after she extends her hand to the girl. Miranda loses consciousness. Miranda next wakes up in the very hospital she works for, but as a patient treated by her co-worker, Dr. Pete Graham (Robert Downey, Jr.). Drugged and confused, she remembers nothing of what happened after the car accident. To her horror, she learns that her husband Douglas (Charles S. Dutton) was brutally murdered and that she is the primary suspect. While Miranda copes with her new life in the hospital, the ghost uses her body to carry out messages (most noticeably, she carves the words "not alone" into Miranda's arm), which leads her former colleagues to believe Miranda is suicidal and is inflicting the wounds on herself.
Following his discovery of the body of his wife (Amy Irving) in a bathtub after her apparent suicide, Dr. David Callaway (Robert De Niro), a psychologist working in New York City, decides to move with his 9-year-old daughter Emily (Dakota Fanning) to Upstate New York. There, Emily makes an apparently imaginary friend she calls "Charlie". Her friendship with Charlie begins to disturb David when he discovers their cat dead in the bathtub, whom Emily claims was a victim of "Charlie". Meanwhile, David suffers from nightmares of the New Year's Eve party that occurred the night before his wife died.
In Los Angeles in 1928, single mother Christine Collins (Jolie) returns home to discover her nine-year-old son, Walter (Gattlin Griffith), is missing. Reverend Gustav Briegleb (Malkovich) publicizes Christine's plight and rails against the Los Angeles Police Department (LAPD) for its incompetence, corruption and the extrajudicial punishment meted out by its "Gun Squad" led by Chief James E. Davis (Feore). Several months after Walter's disappearance, the LAPD tells Christine that he has been found alive. Believing the positive publicity will negate recent criticism of the department, the LAPD organizes a public reunion. Although "Walter" (Devon Conti) claims he is Christine's son, she says he is not. Captain J. J. Jones (Donovan), the head of the LAPD's Juvenile Division, insists the boy is Walter and pressures Christine into taking him home "on a trial basis".
In 1963 Oregon, Randle Patrick "Mac" McMurphy (Jack Nicholson), a recidivist anti-authoritarian criminal serving a short sentence on a prison farm for the statutory rape of a 15-year-old girl, is transferred to a mental institution for evaluation. Although he does not show any overt signs of mental illness, he hopes to avoid hard labor and serve the rest of his sentence in a more relaxed hospital environment.
In 1944, the Nazis build a dimensional portal off the coast of Scotland. With the help of Russian mystic Grigori Rasputin, they intend to free the Ogdru Jahad—monstrous entities imprisoned in deep space—to aid them in defeating the Allies. Rasputin knows this will be an apocalyptic event that he believes will create a paradise. He opens the portal with the aid of his disciples, Ilsa von Haupstein and Obersturmbannführer Karl Ruprecht Kroenen, member of the Thule Society and Adolf Hitler's top assassin. An Allied team is sent to destroy the portal, guided by young Trevor Bruttenholm, who is well-versed in the occult. The German team is killed and the portal is destroyed—in the process absorbing Rasputin—while Haupstein and Kroenen escape. The Allied team discovers that an infant demon with a right hand of stone came through the portal; they dub him "Hellboy" and Bruttenholm adopts him.
In the 1960s, a young woman nicknamed Babydoll (Emily Browning) is institutionalized by her abusive widowed stepfather (Gerard Plunkett) at the Lennox House for the Mentally Insane after she is blamed for the death of her younger sister. The stepfather bribes Blue Jones (Oscar Isaac), an asylum orderly, into forging the signature of the asylum's psychiatrist, Dr. Vera Gorski (Carla Gugino), to have Babydoll lobotomized so she cannot inform the authorities of the true circumstances leading to her sister's death. During her admission to the institution, Babydoll takes note of four items that she would need to attempt an escape.