The episode begins with Emily filling up a form. She then sees that Will is really happy with Cassandra and Cassandra tells her that Will told her that she has been too rude to Emily and since will and Emily are friends, she will try to mend things between them. Cassandra really likes Will. Emily then tells them about the constructive criticism that she wrote on Bandari’s evaluation form where she has penned down that Bandari shouldn’t use her strength to intimidate students as they would be too scared to ask questions and that would hinder the learning process. Will and Cassie are shocked as they tell her that Bandari gets those forms.
Emily tries to get her form back when she is asked by Hamada and Kyle Putnam, a world famous pediatrician to join them. The case is about a three month old baby, Jake, who was admitted for slight fever and unexplained abdominal pain and vomiting. Putnam wants Emily to keep the mother away from him as she is driving him crazy. The mother is really paranoid from reading all sorts on the internet. She then points out to the movements the baby is making with his legs. The father thinks it is normal. Emily finds it worrisome and tells Putnam that the baby is having contortions. Cassie and Emily then watch will performing his first surgery and, Cassie finds him very sexy. She tells Emily that she is going to go crazy on Will tonight. Okay, Emily thinks they should take the whole friendship thing slowly.
She gets a page from Dupre’s office. It is Tyra and she tells Emily that she is ready to tell her father that she is gay. But she wants Emily to stand by her as she knows that he father will not yell at her in front of Emily. Emily sees the evaluation envelopes on the table and takes one which she presumes is hers. Dupre arrives and Tyra tell him that they need to talk. Dupre feels that Emily told her about the affair he had. But before Emily could say something Dupre admits about his affair to his daughter. Tyra walks out. Bandari introduces Cassie and Emily to Peter who has had a number of heart surgeries and now he has developed an allergy to anesthesia. He is now admitted to repair the swelling of the aorta before it ruptures. So Dr. John has found an alternative.
Peter will be awake during an open heart surgery. Peter is a believer in God and Bandari tells him that his life is in her hands. Cassie tells Emily that John is an excellent surgeon. Putnam and Emily examine Jake and during the sonography, Emily explains to the mother about a simple procedure they need to perform on Jake to correct the issue with the intestine which is disrupting Jake’s bowel movements. Putnam looks at the sonography once again and is worried. He tells Emily to call Social services. The woman arrives and explains the real problem to the parents. Externally Jake has male sex organs but internally he has the female sex organs. Now, the procedure to remove the male sex organs is simpler.
Removing the female sex organs could pose a significant threat to Jake’s health in the future. They still need to verify Jake’s chromosomal constitution. But the real problem is how Jake will identify himself; as a boy or a girl. Putnam assigns Tyra and Emily on the case; one to deal with the mother and the other to assist with the child. Cassie figures out that there is something wrong between Tyra and Emily and she tries to fish things out of a pissed Tyra. Will and Micah are attending to the old lady who just had an appendectomy. Emily arrives and hands over the lab reports to Will. Micah sees that Will is growing too confident about himself. Cassie is back to her old ways. She lies to Emily telling her that Bandari has postponed the meeting and it will take place after twenty minutes.
In fact, she made Emily miss the meeting. She did this because Tyra told her the truth that Emily told Will not to date her. So now Cassie is assisting Bandari in the surgery and Emily will end up babysitting. Talking of babies, Jake’s intestine is back to its original structure. Next, the old lady is n pain and she wants Will to give her something to ease it. The lab results aren’t back; but Will takes a call and tells the nurse to give her some meds. At the OR, Emily is talking to Peter and trying to relax him as he is awake during the surgery. He blacks out and his heart stops beating. But Bandari manages to revive him. When later he is told about what happened, he starts hyperventilating.
Emily tells Will what happened and asks him not to tell Cassie about the crush she had on him as Cassie would make her life difficult. Micah puts Will off the case because he prescribed medicines to the old woman without waiting for the results; he jumped protocol. Putnam tells Jake’s parents that Jake is genetically a female but he was exposed to high amounts of testosterone while he was in the womb and now it cannot be determined what Jake would be once he grows up. The best way is allow Jake to grow normally and when he matures, he will identify his gender and then the procedure can be done. The father decides that he doesn’t want his child to grow up like a freak and that he is a boy. He wants the surgery to be done now. Emily realizes that the evaluation paper that she picked up isn’t hers.
She sees Hannah, Peter’s wife walk out crying. She goes to check on Peter. Peter tells her that he has lost all faith after his near death experience and that he has never felt this lost. Bandari asks Emily to fix her mistake as she should have known that since Peter is a religious man; his reactions to such a situation could be extreme. Emily and Tyra iron out their differences. Emily tries to talk to Hannah and tells her that all this too could be a part of God’s plan. Jake has rectal bleeding and so they need to perform a surgery. The father is too upset as he was terrified with the thought of losing Jake. He doesn’t want to put Jake through a situation of this sort and so he decides that they should let Jake grow the way he wants and let him decide.
They will also choose a neutral name for Jake. Hannah is back with Peter and she tells Bandari not to be hard on Emily as she had helped. Emily tells Cassie the truth about her feelings for Will and that is why she had asked him not to date her. Cassie tells Will that Emily told her the truth and that they should keep it professional at work so that Emily is not uncomfortable by seeing them together. Will agrees.
Tyra tells Dupre that she is gay and that she was here to tell him that and that she was scared of being a disappointment to him. But now she doesn’t care about how he feels as he is a bigger disappointment. She leaves and tells Emily that she needs a drink. The episode ends.