In "Newbies," Dr. Shaun Murphy tells his girlfriend Lea Dilallo that the people staring at them are the new resident applicants. Jordan argues with Dr. Marcus Andrews over giving a 17 year old patient a breast implant, leading to him rebuking her for undermining him to a patient. Later, Andrews admits that he actually likes and respects Jordan for undermining him as it shows that she has courage and assertiveness that will serve her well. Andrews states that he told Jordan to stop lecturing him as its easier to teach an aggressive resident restraint than a passive one assertiveness. She ends up being one of the applicants selected for the program.
In "Not the Same," Jordan ends up being one of Shaun's two junior residents alongside Dr. Olivia Jackson. Jordan bonds with their pregnant patient Kenzie whose own body is trying to kill one of her twins. When their attempt to stop the labor after delivering the stronger twin fails, Shaun decides that they must perform a C-section which will doom the remaining twin. Jordan steps in rather than having them pull out restraints and gets Kenzie to focus on the future she will have with her sons. Jordan is able to calm Kenzie down and the labor stops, preventing the need for a C-section.
At the same time, Shaun struggles with being in charge and a mentor to Jordan and Olivia, in particular Jordan. Following advice from Morgan Reznick, Shaun asks Jordan about her problem with authority and she explains that she has a problem with Shaun not acting like an authority and not doing the one thing any junior needs from their supervisor: if she's screwing up, she needs to know that he has her back. Later, Shaun gives Olivia a list of everything she did right on the case as proof that she can hack it and Jordan a list of everything she did wrong as a way of, as she wanted, having her back. Though surprised, Jordan is visibly pleased by this.
In "Lim," Jordan is assigned to perform an abortion, but she refuses due to her religious beliefs. She later changes her mind, but is forced to walk out during the procedure and a short-tempered Lim assigns Jordan to scut work as a punishment. Jordan later admits to Lim that her behavior was not just motivated by her religious beliefs, but the fact that Jordan herself had an abortion, choosing to place her career over motherhood, although Jordan doesn't regret her choice. To Jordan's surprise, a sympathetic Lim places her back on surgery after hearing her story.