Eli takes Nate golfing on the latter's birthday. Eli explains that he'll be representing Jim Cooper's son J.J. in his emancipation filing, and mentions that Cooper threatened Nate's job at the hospital. Eli starts to laugh uncontrollably and then falls to the ground, dead drunk. He looks to find himself as his father in his old home, at Nate's birthday party. The kids call for young Nate, who comes in and is disappointed his dad is drunk. A young Eli is also there. Eli wakes up and tells what Nate what happens.
At the office, Jordan tells Eli to apologize to Cooper and withdrawal from J.J.'s case. Eli isn't happy at having his judgment superseded but Jordan warns that if Cooper leaves then their other clients will follow. Cooper comes in and Eli starts to apologize, but Cooper demands his resignation. Jordan refuses to be intimidated and tells him they're taking J.J.'s emancipation case, and that Cooper needs to get out.
At Posner-Klein, Maggie warns Matt that the upper management is looking for the snitch who told Wethersby-Stone about the mole. She figures that because they know Eli and Taylor, respectively, everyone thinks they leaked the information. They're interrupted when Posner summons both of them into his office.
Eli and Jordan go with J.J. to meet Cooper and his new lawyers: Matt and Maggie. Taylor is angry that Matt didn't warn her the last time they were in bed together. Eli gives them J.J.'s terms and Cooper interrupts, telling his son it's time to go home. J.J. refuses, saying that it's time for his father to let him go. Cooper refuses and leaves.
Patti's daughter Angela visits the office. Keith, trying to avoid her, hides in Eli's office and claims he has a stationary emergency. Eli knows Angela through her mother, Patti, and when he greets her she spots Keith. Patti warns Eli that the medical experts he wants to call have all left the country for expensive vacation... funded by Cooper.
Jordan visits Taylor and talks about the pregnancy. She's checking her waistline and Jordan says that she should tell Matt. Taylor objects but Jordan insists that she needs to be giving her A game in court against Matt and Maggie. Taylor reluctantly agrees to tell Matt.
Matt and Maggie meet in the P-K cafeteria and she tells him that she was the one who told Eli about the mole. Matt realizes that Posner is testing their loyalty by pitting them against Eli and Taylor. Taylor arrives with some discovery files and he says that J.J. is wrong. Taylor snaps at him and then leaves without telling him about her pregnancy.
Figuring that his vision involves Nate, Eli tells his brother that he needs to act as medical expert in J.J.'s emancipation case. Nate warns that Eli has sued the hospital before and won, and the administration isn't thrilled with Nate as a result. Nonetheless he agrees to testify. As he does so, his boss Snyder comes in to watch. Nate testifies that J.J.'s MS is currently asymptomatic and he should be able to function on his own. Matt questions him about the testimony of other doctors and Nate notes that Cooper is using his money to influence. Matt also gets Nate to admit that Matt hasn't examined J.J., and that his MS could flare up without warning.
Patti tracks down Keith and asks him why he's avoiding Angela. He dodges the issue about Angela's cocaine use and says he'll call her. Patti mentions to Eli that she still think something is up between Keith and her daughter. Eli starts acting drunk again and has another vision where he is in his father's body when he and Nate were children. He sees his father writing something about Cooper in his journal of visions, but is interrupted when young Nate comes in and wants to know where his birthday cake is. Before he can read the notebook, Nate yanks it away and says that his father loves Eli more.
Eli goes to see Frank to confirm he burned the notebook. Frank says he did and Eli insists that whatever was in it about Cooper was important. Eli still doesn't believe the visions warning him not to take the Cooper case, noting he's helping father and son. Frank warns that things may not be clear but God works on his own schedule and Eli is taking a big risk by ignoring the Almighty's warnings.
Matt arrives at Wethersby-Stone with flowers and an apology bear for Taylor. Before he can see her, Jordan spots him and assumes the bear is for his pregnant daughter. He mentions the pregnancy and when Matt is shocked, Jordan realizes that Taylor never told him.
Nate's boss Snyder visits him and warns him about testifying against Cooper. Nate questions Cooper's influence and Snyder tells him they want to stay on the philanthropist's good side then leaves. Frank visits and tells Nate that he needs to go back to court to watch the emancipation trial: Mr. Stone's journal says that Nate will do so. Nate does so and watches as J.J. testifies that he has friends, and that his father has tried to undermine him whenever he's disobeyed his instructions. Maggie asks for the judge's permission to let Cooper cross-examine his son. Eli and Taylor object but Maggie argues that if J.J. wants to be an adult, he's going to have to demonstrate he can handle some tough questions. The judge agrees and Cooper questions J.J. about the fact Cooper loves him and wants to keep him alive. J.J. testifies that Cooper kept his wife, J.J.'s mother, alive for an additional six months but she hated him for it. Now Cooper needs to let J.J. go. Cooper asks J.J. about the time he called his father after taking excess medication and ending up in the ER, and blamed Cooper for leaving him alone. Cooper starts to badger him as J.J. breaks down in tears, and Eli demands Cooper stop. In chambers, Eli is angry with Maggie for allowing the cross-examination and Matt is mad at Taylor for not telling him about the pregnancy. Matt leaves and Taylor chases after him, while Eli tells Maggie he doesn't know who she is any more. Nate comes in and tells Eli in private that he saw J.J. displaying MS symptoms: he's getting worse.
Keith visits Angie at the dance studio where she works out and she refuses to talk to him at first. Eventually she warms up and as they discuss music, they kiss. However, he draws back and then tells her about how ADA Jarrells' blood test showed Angela positive for cocaine. She gets angry with him for suspecting her and then shows him that she's taking amoxicillin, which can show up as cocaine on a blood test. Keith tries to apologize but she leaves him.
Nate runs a new MRi on J.J. and finds two lesions that weren't on the most recent MRIs a day or two earlier. He figures that someone Cooper is reusing old MRIs to make it appear that J.J. is asymptomatic so that he can participate in the MS clinical tries, and the hospital is helping him. They call J.J. in, who has already realized he's getting worse. Eli tries to reassure J.J. by explaining how he came to terms with his own illness, and says that he'll have to just get on with his life and have hope.
Both sides meet and Eli shows the opposing counsel the fake MRIs. Cooper insists on talking to J.J. who gets up and leaves. Eli lays it out, that Cooper faked the MRIs to keep his son in the trials and the hospital went along with him thanks to his donations. Matt warns Cooper not to say anything further and Eli informs them they'll have to give in to J.J.'s demands, cut him a check, and clean house at the hospital.
An angry Taylor goes to Jordan, who apologizes. She's almost happy that her relationship with Matt is over, but Jordan notes that Matt has a right to be angry with her for hiding the pregnancy. She says that she needed a break for Eli and deliberately sought out Matt as the most un-Eli person she knows, but didn't plan on having a permanent relationship with him.
Eli visits Frank and wonders what he's missing. He finally figures out that the vision was warning him about J.J., and Eli has Frank bring back the vision using acupuncture. This time Eli realizes that the figure in the burning Cooper laboratory is J.J. Eli goes there just as the building bursts into flame. He goes inside and finds J.J. just where he was in the vision, holding a can of gasoline. Eli gets J.J. out as the firefighters arrive. At the hospital, J.J. admits he wanted to take something, anything, away from his father the way his father took away his chance of competing in the Olympics. Eli tells J.J. that if he wants to be emancipated, he's going to have to grow up and realize there aren't always two opposing sides. Eli leaves, letting J.J. and Cooper talk in private.
Matt comes in to apologize to Taylor, who apologizes to him about keeping the pregnancy secret. He proposes to her, saying he loves her and for the first time wants a normal relationship. She thanks him but turns him down and they kiss.
Keith visits Angie at the hospital school, only to discover that she was suspended several weeks ago.
Nate visits Frank at his shop and asks how Frank knows what was in the journal about him. Frank admits that he made a copy before burning the original. He tells Nate that Eli isn't ready for everything about his future that the book reveals, and asks Nate not to tell. Nate needs to know what the journal says about him, and Frank reads him a note that Mr. Stone left for his son. Mr. Stone saw that Eli will do amazing things, but Nate's love will see him through.
Later that night, Nate meets with Eli, who tells him that the hospital attorneys have agreed to pay Nate a considerable sum of money in return for his silence and his resignation. Nate considers it and Eli thinks that it's a gift from their father, to make up for the childhood he ruined. Nate says there's no amount of money that can do that, and shares a drink with Eli.
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