The episode begins with the police responding to a disturbance involving a Russian-immigrant family, who are very frightened and unresponsive. Police find a murdered man in the apartment and a boy hiding under the bed. The boy, frightened, kills two policemen with a tentacle protruding from his abdomen.
Will Zimmerman, a forensic psychiatrist and former FBI consultant, is called in, but the detective in charge claims they already have the guy who killed two of their own in custody, and that he has a criminal record. Will examines the crime scene anyway and, employing his singular powers of observation and deduction, figures out there is a kid unaccounted for. But the detective does not believe him, insisting there was no kid and that they have eyewitnesses and the shooter. Will counters, saying that there was no shooting. As he's leaving, Will sees the kid on the ledge outside the building. The boy jumps to a fire-escape on the building across the street and Will calls for him to stop, but he runs away. A blond woman on a motorcycle whizzes past Will, apparently chasing the kid. Then Will is accidentally hit by a car. Groggy, he sees a woman who tells him that it's not the way she hoped they would meet. Will loses consciousness and has a dream of himself as a boy being dragged away by a monster.
Will awakens in the E.R. He goes upstairs where the eyewitness is identifying the supposed shooter. She makes a positive ID, but Will notices that she is lying. He confronts her, but she denies it and keeps protecting the boy. Shortly thereafter, the blonde on the bike tracks the boy into the underground tunnels. At the morgue, Helen Magnus, the woman who hit Will with her car, is doing an autopsy on the victims and finds something strange. At the same time, in the red light district, a man materializes out of thin air. He has a medallion with a picture of Helen Magnus. He is looking for a place called the Sanctuary, which takes care of the most unusual guests. A prostitute gives him directions to a place by the water which is rumored to be unusual. The man then kills the prostitute in cold blood.
Will is attempting to convince the detective that the eyewitness is lying, but the detective calls his behavioral science 'woodoo crap' and asks him to back off because that is exactly the sort of thing that got him fired from FBI. Helen Magnus follows Will outside and tells him he is right, that the police have the wrong man and that the boy is real and in need of help. She introduces herself as someone who embraces the full spectrum of reality. She seems to know a lot about Dr Zimmerman, including how his theories were considered so controversial at the FBI that no one believed him. She says she wants Will and gives him a choice: to go back to the world which doesn't appreciate him or to face the truth which he has been seeking ever since he was a child. She gives him a card which says "Sanctuary for All, Dr Helen Magnus, M.D. D.T.C.X.B" and offers him a job. Will declines her offer and goes home, where he has a surprise visit from his ex-girlfriend Meg, also unappreciative of his gifts, who is picking up the last of her things.
Changing his mind, Will calls Helen and she picks him up. Her driver is very unusual. She takes him to the Sanctuary, which has a very high-tech security system. Despite his apparent ability to teleport, the man who murdered the prostitute cannot get in. Helen explains that the boy she is looking for is very special and that she expects to have him there before the night is over. She is reluctant to say whether he's guilty or innocent of the murders. Will tells her that they are wasting each other's time, but she stops him from leaving by saying that his instincts about the boy were right. The boy is anything but normal and her Sanctuary is also filled with creatures that she calls 'Abnormals'. As the leather-clad blonde knocks out two transit cops trying to corner the boy, Helen takes Will on a tour ("Fair warning, Dr, Zimmerman, you're about to leave the world you know behind."), showing him a mermaid and other strange creatures unknown to regular science. Most of the beings in the Sanctuary are there voluntarily because it's their last refuge, however, others are there because they are too dangerous to be left roaming free - but it is a sanctuary for all, not a zoo or a prison. However, Magnus not only helps her charges, she studies them.
Will also meets Helen's driver, who is also her servant and former patient. Will, who believes he looks like a monster, is afraid of him, but Helen says that he's a trusted member of her staff and no threat. Again, Magnus offers Will a job, but he still can't quite wrap his head around the idea that she works "with monsters". Helen explains that these creatures are sentient beings who deserve the same respect as humans and claims they are the key to past and future evolution. Feared, hunted and reviled by society, they are out there, lost, like the boy, in need of help, in need of Will's help. Helen says she needs someone like Will, who sees the world as it is, beyond the surface. She sees great potential in him. She argues that great doctors dare to believe in the unbelievable and to go outside the boundaries of known science.
Helen receives a text from the blonde woman informing her that the boy has been found. Helen and Will enter the underground tunnels. They find the boy hiding in a box and when they approach, Will almost gets hurt by his tentacle - but the blonde saves him. Helen shoots the boy with a tranquilizer. She then introduces the blonde as Ashley, her daughter, which Will finds hard to believe as the two women appear to be almost the same age. Back at the Sanctuary, an incredulous Will learns more about the exploits of the Magnus family as Helen patches up her daughter. Ashley wants to go out in order to pick up some new equipment ("Sylvio has some fabulous new product for me - top of the line Kevlar, prototype hollow-points, digital fuses …"), but Helen insists that she stay in for the night as there have been some fluctuations in the EM (Electro-Magnetic) shield which protects the Sanctuary.
Later, observing the boy from the gallery above, Helen explains that the tentacle is a genetic mutation resulting in a symbiotic appendage. She says that she can't truly help him without first gaining his trust. Will tells her that he can't help because he lacks the necessary experience and training. But Helen challenges him to see beyond the tentacle and help the boy. "If not, then so be it. I'll simply admit that I was wrong about you."