Perception begins its Second Season with Daniel (Eric McCormack) being asked by an Assistant U.S. Attorney (Scott Wolf), and Kate's (Rachael Leigh Cook) soon-to-be ex-husband, to psychologically examine of a man (Evan Jones) convicted of murder who is being retried under his new lawyer's assertion the murderer was never given an mental competency evaluation and may not be fit to stand trial. After talking with the subject and performing and MRI, Kate's expert offers his opinion that their killer, who shot himself in the head after murdering his wife, doesn't technically exist anymore and is now a completely different person.
When the opposing counsel (David Paymer) gets wind of Daniel's findings he decides to call him in as an expert witness to prove that the prosecution is trying to convict a man who no longer exists. The lawyer then proceeds to call in host of character witnesses (Brian Thompson, Ingo Neuhaus, Evan Helmuth) who show the drastically different personalities the man both before and after his brain injury. Seeing his sure conviction slip through his fingers, Kate's ex calls Daniel back to the stand and uses the professor's own psychological history to torpedo his credibility.
After the man still gets off, and is murdered that same day, Daniel begins hallucinating the old version of the defendant (the one he didn't meet) mocking him for getting played. Here we learn Daniel's perfectly rebuilt life isn't quite as perfect as he's been leading everyone to believe. First, he's slowly decreased his dependency on the drugs which had begun to offer unintended side-effects in the form of body tremors. Second, the stress of the trial brings back his old neuroses with a fierceness he's unprepared for. And third, the truth of his romantic relationship with Dr. Catherine Newsome (Kelly Rowan) is called into question when we see his more romantic moments are with his delusion of Natalie, not the psychologist.
As in the show's first season, Daniel's hallucination helps lead Kate to the killer and the episode ends with another lecture by the professor about the nature of a man's brain and how we are stuck, whether we like it or not, with the one we've bee given (including all the imperfections it came with). "Ch-Ch-Changes" is a bit of a tease because by the end the truth of the professor's relationship with Catherine/Natalie is murkier than ever. Despite showing us a Professor Pierce in total control of his faculties it's obvious by the end of the episode that is not the case. However, even with the return of his hallucinations, Daniel is still able to lead the FBI to a killer and prove his worth yet again.
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