The twins suffer complications from their surgery forcing the team at San Jose Boneventure Hospital to make a life-changing decision. Meanwhile, Dr. Shaun Murphy returns to the hospital after his trip with Lea and decides he needs a more permanent change and gives Dr. Aaron Glassman his two weeks’ notice.
Jenny, one of the twins wakes up but the other is stuck in a coma. Shaun Murphy returns to work but Neil Melendez isn't happy how he lied about where he was. Claire Browne and Shaun do an angiogram on Katie trying to find out why she's in a coma. Claire asks Shaun about his road trip. Shaun says that he kissed Lea and that Aaron Glassman is mad at him. Dr. Glassman and Shaun talk about him running away. Dr. Glassman asks if this trip with this girl helped. Shaun says yes and that he'd like to give two weeks notice.
Jenny has a bad experience about being alone. Because for the first time she doesn't have her sister to be there with her. Dr. Jared Kalu tries to get his job back. Shaun suggests a stent to help Katie. Shaun helps the surgeon put the stent into the patient but it doesn't work so they abort the surgery. They learn that Jenny needs a new heart and that Katie is a perfect match. Melendez is against it since Katie is still technically alive. They propose their plan to the mother of the twins. She agrees to the surgery so that Jenny can survive.
Dr. Melendez writes Shaun a recommendation letter. He asks Dr. Glassman to sign it. The hospital decides to settle concerning Kalu's case. Claire talks to Dr. Glassman about Shaun. She says that Shaun thinks that he's mad at him. She suggests he signs the letter since it shows that Dr. Glassman believes in him. They proceed with removing Katie's heart but Katie suddenly stabilizes. The doctors believe that if they reattach the twins that they'll help heal each other. Jenny doesn't want to use Katie as a life support machine.
Claire wants to put the twins back in the same room so that Jenny can see that Katie really is gone. Shaun helps Lea pack. He says that he wants to have his own life, one that he controls. Melendez has a moment with Jessica Preston. Jenny agrees to the surgery after realizing that wherever she goes that Katie will always be with her. The surgery is a success. Shaun and Dr. Glassman finally talk. Dr. Glassman gives Shaun the letter of recommendation. He promises Shaun that if he stays he'll back off and let him make his own choices.
Surprisingly, Katie wakes up but the doctors don't know how. Kalu doesn't want the money. He wants his job back. Claire asks Shaun if the reason he's moving to Pennsylvania because of Lea. He says that she makes him happy. Claire tells him that she'll miss him. Jenny and Katie have to be separated again because Jenny is killing Katie. Katie starts crying because Jenny's health suddenly deteriorates. Jenny dies because her heart had nothing left to give. Katie refuses to separate from Jenny but her Mom comes in and convinces her to let Jenny go. Kalu gets his job back but at a cost. Shaun gives the letter back to Dr. Glassman and decides to stay.
Jessica tells Melendez that she wants to break up. This is because she wants him to have kids and she doesn't. Lea gives Shaun the baseball they packed earlier. She tells him to bring it to her when he visits her in Hershey. Lea and Shaun hug. She tells him that he's a good doctor before she kisses him and leaves. Shaun puts the baseball on his dresser right next to the picture of him and his brother.
- This is the last episode to credit Paige Spara as a guest star. In season 2, she is a series regular.