They find out that Katherine is in Elena's body in The Vampire Diaries Season 5, Episode 14 ("No Exit"). The characters put the pieces together that Katherine is inhabiting Elena's body after receiving a text from Matt that says "help K" instead of "help E," which leads them to realize that Katherine has taken over Elena's body. This discovery is further confirmed when Caroline and Stefan discuss Elena's strange behavior and realize it is Katherine pretending to be Elena. The group figures out the truth and tries to respond accordingly in subsequent episodes.