In high school, C.J suffered from depression and would use alcohol to cope. During one day of binge drinking, he revealed to his friends what he really thought of them. This included the girl he had feelings for. None of them spoke to him afterwards. Because of his hang-ups for the girl, C.J swore off relationships and drinking. Sometime between seasons 3 and 5, C.J is admitted to Boston Bay College where he befriends David and becomes a counsellor at the The Stand, a teen helpline.
C.J later is attending the same party as Jen, Jack, and Audrey, albeit where he is abstaining from alcohol. He spends the night talking to Jen while Jack is with his professor and Audrey is binge drinking to deal with her fight with Pacey. When a blackout drunk Audrey is taken upstairs by a guy, Jen tries to intervene but is stopped by his friend. C.J shoves him out of the way and he and Jen remove Audrey from the premisis and prevent her from being raped.
On Halloween, C.J brings his friend David to a costume party where he meets with Jen and Jack. C.J spends the night hanging out with the latter where he confides in Jack that he doesn't see himself as being in a relationship with Jen. Meanwhile, Jen becomes convinced through meeting David that C.J's lack of romantic interest stems from being gay. David expalins that C.J is indeed straight and Jen continues her sexual advances.
When C.J goes on a 'non-date' with Jen, he winds up comforting a drunken Audrey who spent her evening trashing the local bar Hell's Kitchen while performing with her band. He confides in her about his past as a depressed alcoholic. The two later have sex that night despite Audrey being in a relationship with Pacey. At the No Doubt concert in Worcester, Audrey and C.J get into an argument about what happened between them. Pacey overhears and punches C.J in the face. Jen, now aware of C.J's lack of interest in her, is upset but chooses to be the bigger person and help him ice his face.
After Jen begins to work at the counselling centre and Grams goes on a date with C.J's uncle, Jen and C.J begin dating. At Pacey's house party, C.J decides to take a few shots upsetting Jen. Following the argument, Jen and C.J have sex together for the first time.
Jen unexpectedly breaks up with him when Grams is diagnosed with breast cancer. He assures her that he will be there for her emotionally while Grams undergoes treatment.
By the series finale, five years have passed and Jen and C.J have broken up. It is unclear whether or not her daughter, Amy Lindley, is his or not.