Adam hired Dixie to be Laura's nanny (Brooke's daughter), and Dixie stayed on as a servant after Laura was killed by a drunk driver. Adam wanted a son desperately, but Brooke was unable to give him one. Adam was determined to produce his own blood heir, so he slept with Dixie in the Chandler boathouse and she became pregnant. Dixie gave birth to Junior in 1989, and Adam plotted to secretly adopt him. Brooke would never know the child was his. But when Junior was born, Dixie refused to give him up, demanding that Adam make a choice between her and Brooke. Adam told Dixie she was his choice. Brooke overheard their conversation and was disgusted. She packed her bags and went to Jackson Montgomery, who helped her win half of Adam's fortune. Scrambling to secure his legacy, Adam promised to marry Dixie. He then attempted to drive Dixie insane and get her to commit herself to Laurel Hill, a mental institution. If his plan was successful, Junior would be solely Adam's. Tad realized what Adam was up to and helped Dixie escape from the hospital. Tad and Dixie married in 1989.

In 1990, Tad was presumed dead when a bomb exploded as he struggled with Billy Clyde Tuggle on a railroad bridge after saving Dixie after she was kidnapped. After living in California with amnesia, under the assumed name of Ted Orsini, Tad returned to Pine Valley with Brooke's help in 1993. Dixie and Tad married again in 1995. In 1996, Junior told Dixie he saw Tad kissing Liza. Eventually, Dixie divorced Tad and moved to Pigeon Hollow with Junior. In 1998, Adam got a court order for temporary custody of Junior using Camille Hawkins as a reason. Dixie moved back to Pine Valley with Junior and eventually decided to stay. Lee Hawkins kidnapped Junior and Hayley; Junior escaped with Hayley's help. Dixie and Tad were married a third time in 1999, and Adam became jealous of Tad's influence over Junior. He tried to put Junior in a boarding school, but Tad and Dixie found out in time to stop it.

Things were relatively calm for Junior for most of the next two years. Junior and some of his friends formed a band, called DreamStreet, and won a competition at PV High. But by year's end, Junior began to spiral out of control. Dixie's involvement with Dr. David Hayward sent Junior (who asked to be called J.R.) spiraling out of control. He began to hang around with some questionable schoolmates and his behavior became more troubled. Junior paid a classmate to write a term paper and on several occasions used some colorful language directed towards his mother. With each passing day, J.R. acted more and more like his father, even attempting to bribe a police officer. Things got really out of hand when a high (on Ecstasy) J.R. crashed his father's car into a guardrail, nearly killing himself, Hayley and her unborn baby. In court, J.R. was sentenced to community service and counseling.

Angry that his stepfather Tad had brought Leslie Coulson back to town in an attempt to attack Dr. Hayward, J.R. continued to act out. While walking through the park one night, he met Mary Frances "Frankie" Stone, who shared a joint with him and brought him back to her room at Opal's where they were caught in bed by Frankie's girlfriend, Bianca. Frankie was subsequently found murdered and J.R. was subpoenaed as a prosecution witness. J.R. tried desperately to right his life. However, those around him didn't make it easy. Tad and Dixie and Adam and Liza all experienced repeated marital unhappiness and the teen struggled to deal with his family problems and the regular pressures of being a teen.

J.R.'s world was shattered in spring 2002 when his mother left him with Tad to go stay in Switzerland, and died in a car crash several months later. Dixie had been the only constant in J.R.'s life, and without her he couldn't tolerate either of his fathers. He also clashed with Liza over breaking household rules. His only comfort was Kendall Hart, who was drawn to him in spite of being 10+ years his senior. J.R. enjoyed the shocked reactions around him when his family learned of him befriending town pariah Kendall; she even attended the Martin Christmas party with him. Perhaps sensing that they had no real feelings for each other, they drifted apart soon afterwards.

J.R. became infatuated with Laurie Lewis, a beautiful and mysterious girl his age who seemed to be as confused in life as he was. He learned that her mother was dead and her father worked as a janitor at PV High School. Believing that he was in love, J.R. began spending all his time obsessing over her, even cutting an important interview with Harvard to be with her at the movies. Though Tad, who had grown closer to J.R. again, approved of the relationship, Laurie's father and Adam were outraged. Unfortunately for them, everything they did to try to break J.R. and Laurie up only pushed them further into each other's arms. Young love hit a serious snag when Adam cleverly offered a fully paid Harvard education to Laurie. J.R. was disgusted at his father's shameless machinations and demanded Laurie turn his money down. Laurie, who had never dreamed of such a scholastic opportunity, refused. She and J.R. broke up and in the interim, Laurie kissed J.R.'s brother Jamie, who had been a strong friend and confidant to her. After a few weeks, J.R. realized his stupidity and reconciled with Laurie at the opening for FUSION cosmetics. But moments later, Joni, feeling very spiteful after losing Jamie, blabbed the details of Jamie and Laurie's illicit smooch to him. A stunned J.R. ran away, telling no one, including Tad or Adam, of his whereabouts. After a few weeks of using private investigators, Adam discovered that J.R. was working on a cargo ship for at least the summer, to clear his head and get away from all the problems back in Pine Valley.

J.R. returned to Pine Valley in October 2003, appearing in the middle of The Pit as his two fathers -- Tad and Adam -- nearly came to blows. Adam was overjoyed to have his son back, but that quickly changed when at a family gathering J.R. announced that he'd married a young woman he'd met just three weeks before. That young woman, Babe, had already made her mark on Pine Valley. The night before, a tipsy Babe took Jamie Martin's virginity. J.R. would later reveal that he'd met Babe on night in San Diego at the end of a fog-enshrouded dock. J.R. believed that Babe, who was crying, was going to jump and take her life. Babe, however, said that as bad as things were, she never would have taken her own life. Adam tried to break up the newlyweds' marriage with the help of his house guest, trouble maker Mary Smythe. Adam loathed Babe, who he felt was only after his son's money. Try as they might, Adam and Mary were unable to split the pair up. When Adam found out that Jamie had slept with Babe -- and Babe later found out that she was pregnant -- Adam tried to enlist Jamie into breaking up the marriage. That too failed. As Babe's due date approached, she found herself trapped in the middle of nowhere with Bianca following a storm, Babe called Paul and asked that he fly his medical helicopter to take her and Bianca to the hospital. Paul initially agreed, but later agreed. When he arrived, he helped Babe deliver her baby. He then administered an unknown medicine to Babe leaving her groggy. During this time, Paul staged a chopper crash. When Babe awakened, Paul told her that he baby had died during the crash. However, when help arrived and Babe's family threatened harm to Paul if anything had happened to babe's child, Paul changed his story and said that Bianca's baby had been thrown from the chopper. He had hid Babe's baby in a nearby cabin and planned to give the baby boy to Kelly so that she could pass the baby off as her own. Bianca's babe was then given to Babe, leaving Bianca and her family to believe that her child had been killed.

J.R. and Babe named their baby Elizabeth (nicknamed Bess) Charlotte Chandler, but Babe later changed it to Elizabeth Miranda Chandler, in memory of Bianca's baby. Bess seemed to bring J.R. and Babe closer, especially since their marriage took a hit when Babe's affair was revealed. Bianca was still mourning her baby, when she kidnapped Bess from the hospital, thinking she was taking Miranda home. After Kendall and Ryan found Bianca, Bianca returned Bess to Babe. Babe forgave Bianca and J.R. said he did, but he was more cautious than ever. He wasn't thrilled when Babe told him she wanted Bianca to be Bess's godmother and he even hired a nanny to watch Bianca when she visited Babe. J.R. seemed to be more devoted to his family than ever, until he found out another secret about Babe.

After following Babe's mother, Krystal in the Chandler mansion's secret passageway, Liza found a marriage license that had been stashed behind one of the bricks. The marriage license was proof that Babe had been married to Paul Cramer when she married J.R. When Liza showed the paper to J.R., he immediately confronted Babe, who admitted that she married Paul after a one-night stand, but it had been annulled after Bess was born. J.R. told Babe that he forgave her and even asked her to remarry him. Babe accepted and began planning the big wedding she always wanted.

While Babe was picking out China patterns and lace, J.R.'s forgiveness was nothing more than a phony act. He immediately consulted with Adam and they began to plot their revenge on Babe. J.R. sought the assistance of lawyer, Livia Frye to find out how he could take Bess away from Babe. Livia informed him that he was helpless -- since Babe and J.R. were not legally married, Paul was considered Bess's father. Livia drew some papers up and J.R. had Babe sign them, telling her that the papers would make J.R. Bess's father legally. Once H.R. and Babe were legally wed, J.R. began a plan to get Babe out of their daughter's life permanently, trying to make her sleep with Jamie. The result was that J.R.'s family and friends, with the exception of Adam and (initally) Babe, began to realize that J.R. was turning into his father. With the help of a video doctored to make it look like Babe and Jamie were plotting to kill him, J.R. demanded Babe to sign over full custody of Bess. She did, and left town.

J.R. didn't get to enjoy his status as a single parent for long. Babe left a letter for both J.R. and Bianca that proclaimed the truth, but thanks to J.R., Bianca never read her letter, and J.R. continued to raise Bess as his own. He, Bess and Bianca all went to Florida for a charity event, where Bianca finally learned the truth about her daughter. After attacking Jamie with a pipe, J.R. returned to his hotel room where he planned to flee with Bess, only to be confronted with Bianca. In the ensuing confrontation, Bianca fell from the balcony of his room and ended up in the hospital. They were all returned to Pine Valley, where J.R. continued his plans to flee with Bess, and Bianca got weaker in the hospital. J.R.'s world fell apart when Adam helped to prove that Bess was really Bianca's daughter, and although he tried to flee, Tad managed to stop him and took the baby, taking her to the hospital so that Bianca could reunite with her daughter, which finally woke her up.

Determined to punish Babe for his pain, J.R. began tracking her down, and soon learned she was traveling with Jamie and a small boy -- that he realized was his son. J.R. found the two, but soon found himself in the midst of a custody battle that included Kevin Buchanan, who had been raising the boy for months as his own son. After Kevin bowed out, J.R. was ultimately awarded with custody of the boy (whom he renamed Adam Chandler III), and Babe given only extremely limited visitation. J.R. wanted Babe to have absolutely no access to the boy, and was determined to punish both her and Jamie. He made sure that Jamie was kicked out of school and would never get into any of the local schools. When Phoebe Wallingford died, J.R. was put in charge of her estate, which was to be given to Jamie only if he kicked Babe out of his life. Nothing seemed to work, though, as Jamie was determined to be with Babe. When Amanda Dillon came to town, J.R. soon began enjoying a strings-free sexual relationship with her, and enlisted her in his plot to destroy Babe and Jamie.

J.R. also hired a new nanny for Little Adam, Diana Cole. He was amazed by the resemblance she had to his dead mother, Dixie. She soon confessed that she was Dixie, and although angry at first, J.R. was soon overjoyed to have his mother back. He even began softening toward Babe and Jamie, which was primarily at Dixie's request. Tad tried to prove that she wasn't Dixie, and nearly succeeded, until a DNA test proved otherwise. J.R. began to change, seemingly for the better, and he began to find his way back to brotherhood with Jamie, who had dumped Babe after finding her in bed with Josh Madden. He even began to find his way back to Babe. After Dixie was kidnapped by Garret Williams and returned to confess that she wasn't actually Dixie but rather her half-sister Di (Diana Kirby), J.R.'s world fell apart again. He began drinking again, and during a confrontation with Babe admitted that he had bought a judge off and had all her visitation rights terminated. Babe refused to let him leave alone when he had been drinking and jumped in the car with him, and when he hit Amanda Dillon with his car, Babe took the blame.

Once J.R. remembered that Babe took the blame for his crime, he was again torn over whether she was his lover or his enemy. The two began growing close again, and J.R. was beginning to reconsider letting Babe have a part in his life. He was still sleeping with Kendall intermittently, but was getting closer to Babe. When Babe and Little Adam disappeared after the explosion at the Mardi Gras ball, a series of text messages led J.R. to believe that Babe had run off with Little Adam, and he kidnapped Krystal to get the location out of her, threatening to shoot her (he inadvertently shot Dixie through the door). J.R. felt horrible for his suspicions after learning Babe and Little Adam had both been kidnapped by Janet, but although he offered heartfelt apologies to all of the people he knew felt wronged by him, he couldn't forget his suspicions that Babe was playing him. He went to see Janet at the jail, and she continued to insist that Babe was out to get him. J.R. remarried Babe, but couldn't shake his suspicions. Finding out that Dixie was alive and well and had been for years broke him, and he fell back into the bottle.

With everything in his life falling apart again, J.R. couldn't shake the feeling that everyone (including Babe) was out to get him. He overheard part of a conversation between Babe and Krystal and became convinced his wife was out to take their son and break his heart, and concocted a plan to kill her by having construction materials fall on her at Fusion. Unfortunately, Kendall had offered to try to talk to J.R. on Babe's behalf, and she was the one who was caught under the debris, which landed her in the hospital, and put her unborn child's life at risk. J.R. was horrified that he had hurt his best friend, and initially angry that Babe had survived. Babe soon figured out what her husband had been trying to do and confronted him. J.R. finally realized it was time that he stop lashing out at everyone and was prepared to take his punishment, but Babe covered for him in court, getting him off. Although he and Babe soon began to work on their relationship, J.R. again began lashing out at the people around him, joining forces with Jamie to bring down Josh Madden in the hopes that they could get a clue to their missing half-sister's whereabouts.

J.R. found out that Babe had a one night stand with Josh Madden and this upset him. One night, J.R. threw himself out of a window and nearly died. Josh happened to be on the scene and saved J.R.'s life. J.R. would encounter even more heartache when his mom, Dixie, died when she ate poisoned pancakes that were meant for Babe, courtesy of The Satin Slayer. J.R. became just as equally devastated when Babe "died" at the hands of The Satin Slayer. Babe was actually alive and the town, but J.R. didn't find out until later.

J.R. formed a plan in which he would have some employees of Chandler Enterprises "kidnap" him to get revenge on Adam for his kidnapping Jenny Martin a couple of months earlier. J.R. got Amanda involved in his scheme and his "kidnappers" demanded a high ransom for J.R. and Amanda's release. Adam forwarded the money to the "kidnappers." J.R. told Amanda he had the kidnapping staged to get even with Adam and she slapped him. However, Amanda soon started to fall in love with J.R. but not all was happy when it came to Adam and J.R. since Adam said J.R. was dead to him. Eventually, Adam and J.R. reconciled and continued their relationship as father and son.

One night, Richie Novak stole J.R.'s car and hit Zach Slater with it. J.R. was drunk the night this happened and did not know who stole his car. The truth came out that Richie stole J.R.'s car and hit Zach Slater. Richie did other horrible things to J.R., as well. He had him kidnapped since he found out that J.R.'s bone marrow was a match for his and Richie needed his bone marrow to treat his leukemia. Richie thought that J.R. would not donate his bone marrow but J.R. said that he planned to donate it all along. Richie made it look like J.R. had slept with a hooker and this caused a rift between J.R. and Babe. Babe, who believed Richie was a good guy for many months, went undercover as a prostitute to prove that Richie set J.R. up and she succeeded.

J.R. proposed marriage to Babe and they planned to move out to California to get married there and make a new life for themselves and Little Adam. However, Adam sent subpoenas to both J.R. and Babe to have them come back to Pine Valley to testify in a legal case resulting from the Bella perfume being tainted. When J.R. and Babe returned to Pine Valley, several tornadoes touched down on the town and Babe died as a result.

After Babe's death, J.R. started to become vulnerable into turning to alcohol for comfort. David Hayward, having just returned to town, schemed with Amanda Dillon to have a sober J.R. fall off the wagon so he could get custody of his grandson, Little Adam. David paid Amanda to get J.R. to drink, which J.R. did, but Amanda started to tell David she no longer wanted to be part of the scheme.

Amanda became pregnant and was not sure who the father of her baby was. She claimed that it was J.R.'s child but, when Frankie Hubbard ran an ultrasound on her baby, he told her the date of conception and Amanda realized the child was David's. Amanda had Frankie change the date of conception to make it look like J.R. fathered Amanda's child. Krystal Carey found out about this but Amanda and Jake, who also knew the truth about Amanda's baby, convinced her to keep quiet to J.R. Krystal agreed to keep this a secret from J.R. David, one day, confessed to J.R. that he had paid Amanda to get him drunk so he could get custody of Little Adam. Amanda told J.R. that what David said was right. Despite this, J.R. was still on good terms with Amanda. That did not last long when David revealed to J.R. that he, not J.R., was the father of Amanda's child. Amanda confirmed this to J.R. and J.R. swore he'd never have anything to do with her again.

Adam was concerned J.R. would turn to alcohol when Amanda moved out. J.R. poured a glass of scotch in front of Adam, but did not drink it. He wanted to prove he was committed to sobriety. His son, Little Adam, found the glass and drank the contents. Krystal found Little Adam unconscious on the floor. Little Adam recovered, but he was placed in protective custody with Angie and Jesse Hubbard. Although J.R. considered kidnapping his son and taking him out of the country, he fought David through the legal system and was awarded custody. Krystal's testimony was extremely beneficial to J.R.'s case. Her testimony supported J.R. instead of David. Adam had blackmailed her into supporting J.R.

The information Adam had used to blackmail Krystal had an impact on J.R. when it became public. Marissa, the supposed daughter of Krystal's friends, was actually Babe's twin sister. Krystal sold Marissa at birth. J.R. was fascinated with Marissa and enjoyed spending time with her. Although Marissa and Babe were not identical, he saw brief glimpses of Babe in Marissa. Not everyone was pleased J.R. and Marissa were becoming close. Marissa's father, David, did not want another daughter of his involved with J.R. Someone else did not want them getting close; J.R.'s cousin, Scott Chandler. He was also interested in Marissa. Regardless, J.R. and Marissa continued to spend time together. J.R. made a move and kissed Marissa, but soon after admitted he had been thinking of Babe. Although Marissa was disappointed, she forgave him.

J.R. had serious concerns about his father. Adam had been acting strangely since the death of his twin brother Stuart. Someone had wanted revenge against Adam, but mistook Stuart for Adam when they shot the wrong brother. Instead of leaning on family, Adam bonded with a woman several years his junior, Annie Lavery. On the night of Stuart's murder, she had protected Adam. Annie had a history of mental instability, but Adam helped secure her freedom from Oak Haven by providing her with a place to live. The court had a stipulation which banned children from living in the same household as her. This forced J.R. and Little Adam to move out to the yacht club. J.R. could not understand why his father would choose a woman he barely knew over his own son and grandson. It became J.R.'s mission to expose Annie as a gold-digger to his father using any means necessary, including kissing her. Annie knew what J.R. was up to and pushed him away. The connection between Marissa and J.R. continued to deepen, even when J.R.'s health declined. Friends and family were quick to accuse J.R. of drinking again, but Marissa simply offered support. J.R. was diagnosed with a rare form of cancer. It had been less than a year since Little Adam lost his mother, and J.R. vowed not to allow Little Adam to lose another parent. J.R. wanted to keep his diagnosis secret. He was concerned David or Adam would use his illness as an opportunity to gain custody of Little Adam. He only confided in his step-father, Tad Martin, who became his support system. Tad encouraged J.R. to tell Marissa the truth, especially after hearing J.R. call out for Marissa during chemotherapy. J.R. realized he was falling in love again. He took Marissa to a cabin in the woods and told her the truth about his cancer. She agreed to help keep his secret.

J.R. courted Marissa over chemotherapy and doctor appointments and they fell in love. J.R. proposed to Marissa and they decided to elope. Marissa hesitated to say yes. She had only known J.R. for a few months, but the loss of Marissa's adoptive parents and J.R.'s battle with cancer convinced her to take a chance on love. Tad officiated the ceremony, which took place at the Martin's home. Krystal and Little Adam were witnesses. The newlyweds honeymooned at the cabin in the woods, the same place where J.R. told Marissa about his illness. J.R. carried his bride over the threshold of the doctor's office to a chemotherapy appointment.

The prognosis for J.R. seemed to improve temporarily, but then took a bleak turn. He needed a bone marrow transplant. Marissa officially adopted Little Adam, and he decided he wanted to be called A.J. While they waited for a potential donor, J.R.'s heart stopped. He was revived, but he needed a donor immediately. J.R.'s savior came from an unlikely source, his father's wife, Annie. Although J.R. and Annie did not get along, she agreed to be his donor. An old friend of Adam's, Brooke English, had returned to town and threatened Annie's marriage. She saw the bone marrow donation as a way to reconnect with Adam. The identity of the donor was kept hidden from J.R. His family believed his hatred of Annie would stop him from accepting her as a donor.

When J.R. made a full recovery, he learned Annie had been his donor. This knowledge did not change his opinion of her. Instead, he decided to use the bone marrow donation against her by allowing her to believe he was grateful so she would let her guard down. J.R. hoped she would admit she was only with Adam for his money and power. Marissa was frustrated with J.R.'s obsession of exposing Annie. Marissa urged J.R. to be grateful for his healthy status and to make their family; J.R., Marissa, and A.J., the focus. J.R. asked Annie to accompany him on a business trip to Washington D.C. He planned to seduce Annie to prove she did not love Adam, and then reject her. His plan backfired when he realized he was attracted to Annie and did not reject her. He could not use their time together to break up his father's marriage, because it would mean the end of his. He had sex with Annie.

Annie and J.R. decided to keep their night together a secret, but J.R. could not stop thinking about Annie. She could not stop thinking about him either. They taunted and dared one another to repeat the affair. Annie undressed with the door open, knowing J.R. was watching. He swore he did not care about her, but would kiss her. Their dares and threats landed them in a compromising position. Adam walked in on them about to make love. Adam left town with Brooke and handed over control of Chandler Enterprises to Scott. Not knowing what had really happened, Marissa comforted Annie. The divorce papers from Adam claimed Annie had been unfaithful. Marissa incorrectly assumed Annie had slept with Scott. When Marissa learned the truth, she moved out.

J.R. pleaded with Marissa to give their marriage another chance, yet he continued to work with Annie. When Marissa moved back to the mansion, she did not move back into J.R.'s bedroom. He was troubled by the relationship forming between Annie and Scott. They shared a secret, and J.R. was jealous. Scott had stolen Palmer Cortlandt's nanotechnology and marketed it for Chandler Enterprises. Annie was Scott's confidante. Marissa sensed J.R.'s jealousy of Annie and Scott, but J.R. continued his claim he wanted to get their marriage back on track. At the same time, J.R. continued to want Annie. When Marissa tried to spend time with J.R., he often made excuses to work so he could be with Annie. When J.R. asked Annie to become his mistress, she declined.

Despite her feelings, Annie decided to marry Scott, and they became engaged. Annie swore she loved Scott, and Marissa was relieved. J.R. and Annie continued to have intense feelings for each other, but they swore they would not act on them. Marissa misinterpreted a moment between Annie and J.R. at the cabin she and J.R. honeymooned at. Marissa told Scott what she believed she had seen. Scott and Marissa engaged in revenge sex. Annie forgave Scott, and J.R. was willing to forgive Marissa, but she moved out. J.R. asked Annie not to marry Scott, but she did not listen. After Annie and Scott married, J.R. and Annie continued their affair.

When Scott was sent to prison for the theft of Palmer's nanotechnology, Annie and J.R. were free to be together, except they were not. Marissa was fighting J.R. for sole custody of A.J., and J.R. knew a public affair with Annie would compromise his case. The affair between Annie and J.R. continued in secret, but Marissa was suspicious. J.R. decided to warm Marissa up to the idea of shared custody by reminding her why she had once loved him. Annie witnessed the interactions between Marissa and J.R. They were spending more time together as a family with A.J., and J.R. was becoming close to Marissa again. J.R. was torn between the two women. He was drawn to Annie, but he began to long for Marissa and the life they had shared.

Annie began to lose her hold on reality. She was convinced J.R. and Marissa were going to reunite and became extremely jealous. During a hallucination, Annie attacked Marissa. J.R. was concerned for Marissa and canceled his plans with Annie to care for her. This pushed Annie farther. J.R. was warned by Annie's ex-husband that she was becoming unstable, but J.R. ignored the warnings until it was almost too late. Annie locked Marissa in the attic of the Chandler mansion and created a gas leak. She wanted to permanently remove Marissa from J.R.'s life. J.R. rescued Marissa and made arrangements for Annie to be committed to Oak Haven. J.R. tried to get his family with A.J. and Marissa back.

Marissa was reluctant to trust J.R. again but he refused to give up on her. J.R. helped Marissa in her first case as an attorney when she represented Bianca Montgomery in a custody suit. J.R. hired Bianca's ex-wife for a position that would demand more time than a single mother could dedicate. Marissa was grateful to J.R. when Bianca was awarded full custody of her daughters. J.R. recognized Marissa and Bianca had developed a friendship and he took advice from Bianca about how to win Marissa back.

J.R. believed he and Marissa were on the path to reconciliation when she moved back into the mansion. Marissa claimed she needed a temporary refuge from Tad's home so she would not have to lie about the state of Tad's marriage to immigration officials. J.R. continually tried to take his relationship with Marissa beyond friendship but she pulled away each time they started to get close. He started to believe he and Marissa may never reconcile. He shared his relationship woes with Amanda Martin and they had unprotected sex during a one night stand. Afterwards they agreed what they had done would remain secret.

Shortly after J.R.'s night with Amanda he was pleasantly surprised when Marissa showed up in his bed. They slept together and J.R. thought he and Marissa were reuniting. J.R. was worried his relationship with Marissa would be over before it started when Amanda confided that she might be pregnant. J.R. convinced Amanda not to reveal they had been together until she had taken a pregnancy test. He was briefly relieved when Amanda learned she was not pregnant until she informed J.R. she had a sexually transmitted disease that could cause cervical cancer. J.R. did not tell Marissa about his night with Amanda even after Amanda told her husband.

Marissa pulled away from J.R. and he accused her of being in love with his cousin Scott. She shocked J.R. when she admitted she was in love with someone but it was not Scott. She told J.R. she had fallen in love with Bianca. When J.R. questioned her, Marissa admitted she had only ended up in his bed because she had been scared to enter a relationship with a woman. The declaration of love Marissa had made for Bianca pushed J.R. back to drinking.

Tad immediately recognized J.R. had been drinking and implored him to attend an AA meeting before his life spun out of control. J.R. did not follow Tad's advice and instead continued drinking. While heavily intoxicated, he stumbled upon an unconscious woman in the park and shared his problems with her. J.R. recognized that the unresponsive woman was his mother Dixie but he believed he was having a vision of her.

Tad made several more attempts to aide J.R. in reclaiming his sobriety so J.R. could be a good father to his son. A.J. realized something was wrong with his father and he wanted to stay with Marissa instead. J.R. accused Marissa of trying to poison his son against him. J.R. argued with Marissa and Bianca while he was intoxicated. The women confiscated J.R.'s keys but he managed to sneak the keys to Bianca's car and he drove the car into a tree. No one was hurt and Tad convinced the police not to investigate what had happened.

J.R.'s reckless behavior prompted Marissa to get a restraining order which prevented J.R. from having contact with his son until he attended rehab. In the aftermath of the restraining order, J.R. continued to drink and got in an altercation with a man at Krystal's and then shoved a police officer. J.R. begged Tad to help him out one more time, but Tad refused to clean up the mess J.R. had made and watched as J.R. was taken in to police custody.

After J.R. was released from jail, Tad paid him a visit. He told J.R. to sober up and visit him at his house. Tad warned J.R. that if he did not show up, he would regret it for the rest of his life. J.R. arrived at Tad's home and found Tad with Dixie. J.R. initially believed Tad hired someone to pretend to be his mother in an attempt to sober him up. Tad and Dixie explained David had used his experimental Orpheus Project to bring Dixie back from the brink of death. J.R. did not believe the story and went home to continue his drinking. Dixie followed him home and decided to match J.R. drink for drink. He changed his mind about the woman being an imposter and he refused to allow his mother to compromise her heart by consuming alcohol.

J.R. blamed Dixie for the mess he had made of his life and instructed her to leave. He accused her of always leaving him and questioned when she would disappear again. Dixie apologized and told J.R. she was moving in with him and would help him regain custody of his son. He hired Liza to represent him and he arranged for the custody case to be moved up. J.R. continued to secretly drink and he tried to bribe the judge that would be overseeing the hearing. Unbeknownst to J.R., the judge had a reputation for standing up publically against bribes. The judge granted Marissa full custody of A.J.

Liza refused to represent J.R. any longer and J.R. told his mother he was ready to make changes to be the father that A.J. deserved. When J.R. was alone, he spoke to a picture of his father and vowed to make Marissa pay for taking his son. He arranged for a camera to be hidden in Marissa's room and it recorded Marissa and Bianca having sex. J.R. threatened to make the tape public if Marissa did not hand over custody of A.J.

Scott, Colby, and Liza all learned of J.R.'s plan to blackmail Marissa with the sex tape and they warned J.R. he had crossed the line. Marissa and Bianca told J.R. they would not give in to his demands and pointed out that A.J. would be hurt the most if the tape became public. Marissa warned J.R. he needed to get his anger in check before he would be allowed to visit with A.J. Dixie and Tad agreed with Marissa and they reminded J.R. of his childhood memories with Adam as his father.

The bad news continued to mount for J.R. Papers arrived that declared the Chandler mansion was in foreclosure and everyone needed to vacate the premises by the next week. Colby offered to call Adam for help but J.R. insisted he would take care of the company and the house, along with regaining custody of his son. Dixie and Tad offered J.R. a place to stay but he insisted the Chandler home was his birthright and he would not leave it without a fight.

J.R. also learned his father had written him out of his will and he secretly took one of Adam's guns and packed a bag. He stopped by Tad's house and found A.J. in Dixie's care. He persuaded his mother to give him a few minutes alone with his son and he instructed A.J. to quickly grab his favorite toys for a special father/son adventure. Dixie heard J.R.'s plan to run away with A.J. and she pleaded with J.R. to remain in town. She told J.R. if he left town he would miss out on seeing Babe. His mother claimed she had seen a woman with blonde hair at David's Orpheus clinic before she had escaped.

At first J.R. believed Dixie's comment was a ploy to keep him in town until he remembered the time David spent alone with Babe's body following her death. J.R. left without A.J. and immediately confronted David. He demanded to know if Babe was alive and where David was holding her. David refused to admit if he had saved Babe or not but he swore he would never let J.R. near her if she was alive.

J.R. pretended to leave and he witnessed David provide Griffin Castillo with information about a presumed dead resident of Pine Valley. He followed Griffin to the Orpheus site but Griffin injected J.R. with a syringe and he passed out. When J.R. regained consciousness, the site was empty and he returned to confront David. J.R. pleaded with David to tell him if Babe was alive but David only assured J.R. he would never see Babe again.

J.R. made one more attempt to kidnap A.J. when he learned Marissa and Bianca were attending a family barbeque at the Slater home. J.R. sneaked into the house and called A.J. over to him while the adults were distracted. Erica Kane happened upon J.R. and A.J. and she sent A.J. to another room and warned J.R. to leave immediately. J.R. threatened Erica and warned her to stay out of his way. He left without A.J. when Zach Slater, Ryan Lavery, and Jack Montgomery entered the room.

The gun was still with J.R. when he returned home and had a vision of Babe. She reminded J.R. of the good that was inside him and reminded him he still had time to change his ways. J.R. questioned if his vision was real but Babe insisted he would have known in his heart long ago if she were still alive.

After the vision of Babe disappeared, J.R. headed downstairs and was greeted by Adam and Brooke. They returned from Paris to see the mansion one last time. J.R. assumed his father wanted to berate him for his mistakes and he sarcastically thanked his father for cutting him out of the will. Brooke defended Adam and explained Adam had intended to give J.R. freedom from the money and power that had corrupted him.

J.R. insisted Adam wanted to punish him and he had left Pine Valley so he could avoid seeing the disappointment J.R. had turned out to be. J.R. shared that he planned to leave town and Adam agreed that would be J.R.'s best option. J.R. privately remarked that Pine Valley had no idea how bad he could be as he held the gun in his hands.

Before heading out of town, J.R. stopped to say goodbye to his mother and Tad. He congratulated them on their engagement news and said goodbye to A.J. He explained to his son he needed to go away for awhile to fix his recent mistakes. When J.R. walked outside, he pulled out the gun and commented that it would fix everything.

J.R. then headed to the airport and continued his plans to leave town. Dixie and Tad tracked J.R. down and urged him to remain in town because David's mystery patient was revealed to be Stuart. They told J.R. that David's Orpheus Project had saved Stuart and Adam was throwing a party at the mansion to celebrate. J.R. thought the news was a ploy to keep him in Pine Valley and he sent Dixie and Tad away.

J.R. skipped his flight and instead secretly returned to the Chandler mansion. He hid in a passageway on the other side of the party with a gun. He looked at several of the party guests one by one before firing a shot.

Time advanced five years between the final episode on ABC and the first episode of Prospect Park's online version.

Five years later, J.R. was checked on by doctors and visited by family members as he lay in the coma he had been in for the past five years since he had been shot by David. When David was released from prison, he paid J.R. a visit and tried to kill him. J.R. awoke from his coma soon after and asked for Marissa. He was unable to remember that he had shot and killed her and he was diagnosed with retrograde amnesia. J.R. was shocked to see how much his son A.J. had grown and was stunned to learn that Adam had left Brooke English in charge of Chandler Enterprises.

J.R. was released from the hospital and moved back into the Chandler mansion. Doctor Cara Castillo made home visits to assist J.R. with his post-coma physical therapy and he admitted that he remembered what people had said while he was in his coma, including Cara's admission that she had given birth to David's son but had allowed David to believe that she had suffered a miscarriage. J.R. assured Cara that her secret was safe and he made arrangements for Cara to spend time with her son.

While J.R. continued to work on his recovery, he struggled to accept that he was not in charge at Chandler and believed it was because he unable to walk without assistance. J.R. also experienced difficulty in relating to his teen-aged son and accused A.J. of taking steroids. A.J. claimed innocence and J.R. began using the steroids to speed his recovery. Meanwhile, Brooke hired Dimitri Marick as the head of Chandler's media division and they planned a gala to garner attention. J.R. convinced Brooke to allow him the chance to prove himself and he was given a position within the company.

Meanwhile, as J.R. continued to use steroids, he moved Cara's son into the mansion under the guise of being related to the new Chandler cook. He also prepared his presentation for the gala as his steroid-induced rages became more frequent. On the night of the event, J.R.'s file which contained his presentation was erased. He publically accused Brooke of sabotage until his father stopped his rant.

After the disappointment of the presentation, J.R. expressed his romantic interest in Cara and they shared a kiss but she refused to get involved with him since he was her patient. That same night, Cara's son was hospitalized after he suffered an allergic reaction. Soon after, Cara learned that J.R. had stolen her prescription pad and used it to get ahold of steroids, but he also paid her son's medical bills. J.R. asked for another chance but she was unable to trust him. After Cara's rejection, he started plotting his next move toward regaining control of Chandler Enterprises. J.R. also reached out to his son but A.J. declared that he wanted nothing to do with him.