"Classroom of the Elite" is built on a foundation of major twists that redefine the characters and plot. The first key reveal is that the protagonist, Kiyotaka Ayanokoji, is not an average, apathetic student but a product of a secret eugenics-like experiment called the White Room, making him a manufactured genius with unparalleled physical and mental abilities. His monologue at the end of Season 1, where he declares that all people are tools, confirms his manipulative and cold-hearted nature, reframing all his previous actions as calculated moves.
Another significant twist is the true personality of Kikyo Kushida. Her friendly, popular girl persona is a complete facade hiding a deep-seated resentment and a history of destroying her previous class. She becomes a recurring antagonist, consistently selling out Class D's secrets in an attempt to get Horikita and Ayanokoji expelled. The series also reveals that Ayanokoji's father is the head of the White Room and is actively trying to get him expelled from the school to bring him back to the facility.
The climax of the second season reveals Ayanokoji as the mastermind behind all of Class D's victories to Kakeru Ryuen, culminating in a brutal fight where Ayanokoji easily overpowers Ryuen and his gang, forcing him into submission. It is also revealed that Arisu Sakayanagi, the leader of Class A, knows Ayanokoji from the White Room and sees him as a 'false genius' whom she, a 'true, natural genius,' is destined to crush. Ayanokoji's relationship with Kei Karuizawa is another major development; he intentionally puts her through psychological torment to break her dependence on others and build her into a loyal pawn, which eventually blossoms into a genuine, albeit complex, romantic relationship, as she becomes the only person he truly confides in.