'''Season 1, Episode 8''':
!The Equation

While helping fix a woman's car engine on the side of the road in Middletown, Connecticut, Andrew Stockston sees a sequence of red and green flashing lights and is hypnotized into a suggestive state. Upon waking up, he does not have any memory of what happened while hypnotized, but sees that the woman and his son Ben, a young musical prodigy, are missing. Broyles reveals that similar cases have ended with the victims being returned, but left insane from the trauma of the incident. All the victims were academics and accomplished in their respective fields.

When interviewing Andrew, Olivia learns that nine months previously, Ben survived a car accident with a new, extraordinary ability to play the piano, despite never taking lessons. Walter recalls memories of red and green lights, but he's unable to remember more. While trying to dredge up the old memories, Walter recounts a previous unsuccessful mind control experiment he had worked on for an advertising agency, who wished to compel customers to buy their products using flashing lights. He deduces that someone succeeded in producing the lights using wavelengths, and these caused Andrew to sustain a "hypnagogic trance" that allowed his son to be abducted. He successfully tests an experiment on Peter.

Andrew's sketch leads to the identification of the kidnapper as Joanne Ostler, a MIT neurologist who was previously believed deceased. Joanne tricks Ben into helping her complete an unfinished equation by using the image of his mother, who died in the car accident. Meanwhile, Walter suddenly remembers that he heard about the lights from former mathematician Dashiell Kim, a fellow inmate at St. Claire's Hospital, who disappeared under similar circumstances. To discover the child's whereabouts, Olivia encourages Walter to return to St. Claire's. The visit does not go well, and Walter is held by hospital administrator Dr. Bruce Sumner, who remains unconvinced of Walter's sanity.

Peter figures out Joanne's assumed name using a FBI database, while Walter manages to convince Kim into giving up a vague description of Joanne's whereabouts by telling him there is a little boy who needs their help. Kim says he was kept in "a dungeon in a red castle." Olivia and Peter use the information to find the boy once they arrange for Walter's release. However, Joanne escapes with the completed formula, which she gives to Mitchell Loeb. Loeb kills her, but not before using the equation to allow him to pass through solid matter.

!!Tropes
* AssholeVictim: Joanne Ostler, at the ends of Mitchell Loeb.
* BitchInSheepsClothing: Joanne. If her abduction and subsequent manipulation of Ben is any indication, she first shows up like a troubled lady needing help, then hypnotizes and kidnaps the person. Then, she asks them to complete the equation their own way, using her MindControlDevice to put them in LotusEaterMachine, promising gifts and the return of deceased loved ones. When they can't solve it, she resorts to Mind Raping them into insanity.
* CatFight: Olivia vs Joanne. She gives a well-deserved beatdown.
* ConvenientComa: Ben's coma after the accident
* ForeShadowing: [[spoiler: Walter's hallucinating with a clone of himself in the asylum. It's the first clue to the AlternateUniverse plot, but also of how the BigBad will be his alternate version, Walternate.]]
* GoAmongMadPeople
* KarmicDeath: Joanne managed to complete the equation and escape Olivia. Just after she gave it to Loeb, he shot her for unknown reasons. After mind raping Ben, Dr. Kim and so many others, she totally deserved it.
* MadMathematician: Dr. Kim
* MoreHypnotizableThanHeThinks: Peter
* MindControlDevice: Green and red lights
* MindRape: Once Joanne can't get what she wants out of Ben, she sets the machine to turn his dream into a nightmare by watching his mother slowly dying. As seen with Dr. Kim, this usually drives a person insane.
* RoomFullOfCrazy: Photo of murder scene. Basically, Kim's wife bludgeoned to death, and the equation painted on the walls around her, [[CouldntFindAPen apparently with her blood]].
* TheCakeIsALie: Ben's mother isn't real. Joanne kidnapped Ben and strapped him down on a equipment that puts him in a Lotus Eater Machine. The machine makes Ben think his mother is alive, so Joanne can convince him to complete the music/equation. Once he can't, she programs the machine to turn the Lotus Eater Machine into a PsychologicalTormentZone, inducing MindRape by forcing Ben to see his mother slowly dying. She did the same thing to Kim and the others she kidnapped, driving them insane.
* ThemedAliases: Joanne Ritz. Peter claims he also used these, centered in chess pieces(Peter Knight, Peter King, etc.).
* TraumaticSuperpowerAwakening: Ben's musical abilities after the accident
* YouHaveFailedMe: Joanne's reaction to her victims being unable to solve the equation is MindRape them into insanity. And since she seems to do it at the first sign of hesitation or difficulty, it's no wonder it took her ten years to finally solve it, and just short of driving yet another victim crazy, [[HarmfulToMinors a child]] [[WouldHurtAChild even]].
* YouHaveOutlivedYourUsefulness: Probably the reason Loeb kills Joanne at the end of the episode.