The Scrubs third season tells about J.D.’s, Elliot’s and Turk’s experiences during their third year stay at Sacred Heart and second year as residents. In the beginning of the season, with the Janitor’s help, Elliot chooses to set a different image. J.D. likes Elliot again, but has Jordan’s sister, Danni (Tara Reid) for a girlfriend instead. Meanwhile, Danni still has deep feelings for her ex-boyfriend. Turk and Carla get engaged and are preparing for their wedding. Dr. Grace Miller (Bellamy Young), who sees Turk as a sexist and abhors him, is the new attending surgeon in town.

For the whole season, Turk, Todd and the rest of the surgical residents try to deal with her. Dr. Cox and Jordan’s relationship with each other is going smoothly, as well as their relationship with their son, Jack. However, Dr. Cox suddenly starts to be strongly infatuated with Dr. Miller. To add to this, he tries to cope with his best friend’s death. Elliot and Sean Kelly (Scott Foley) have a serious relationship together and struggles to fight for their relationship, despite being far away from each other for six months due to Elliot’s stay in New Zealand.