After Marlena got the encrypted disk back from Philip, she urged John to take a look at it, believing it could help him remember his past. Ava, however, urged John to destroy it and leave the past where it belongs. A conflicted John broke the disk and destroyed the lab, devastating Marlena.
Paul's body was soon rolled into the river, and it appeared as though he was dead. His daughter, Morgan Hollingsworth, marched into the living room of the DiMera mansion and demanded to know from John where her father was, even threatening to kill John. When she reached into her purse, Ava Vitali’s goon, Eddie, pulled a gun on Morgan. Philip arrived and stepped in front of Morgan, taking the bullet. Little did Morgan know that John had Paul all along in the DiMera basement. John wanted to get back at Philip for planting cocaine on his ship and for setting fire to the warehouse, which Paul was guilty of.
John's life took a dramatic turn after Ava made love to him one last time before jumping bail and skipping town. Shortly after Stefano woke up from his coma, The Phoenix vowed revenge on Marlena and had one of his goons inject her with a paralyzing toxin. Fortunately John found her in time and administered CPR, saving her life. John threatened Stefano's life and stayed by Doc's side, realizing how much he cared for Marlena. During this time, John received a ghostly visit from Santo DiMera, a young Stefano, and one from his former persona. John was clearly moved to tears by his ghostly visits and was encouraged not give up on Marlena.
Kayla was able to administer the proper antidote and save Marlena. John expressed how he was ready to work on their marriage. He and Marlena ended up making love in her office, and she reluctantly agreed to come back to the DiMera mansion with him for one night.
In the meantime, Paul pleaded guilty to planting cocaine on John’s ship and to setting fire to the warehouse. He also kept quiet about John keeping him hostage and denied that Philip coerced him into committing the crimes, since Stefano threatened Morgan's life. John was free and clear of all charges, but knew Stefano wanted something in return: to remain silent about everything that went on in the laboratory.
John soon began having headaches and seizures, and even attacked Trent Robbins when he showed an interest in Marlena. Kayla examined John's brain scan and found some abnormal results which would require more testing in order to figure out a treatment pattern. John refused any further treatment, so Marlena continued with divorce proceedings. John even gave up control of the DiMera empire, professing that he loved Marlena enough. It wasn't enough for Marlena and the two still legally divorced.When John's son Brady returned home from Austria after being in drug rehab, he had no memory of his son and no interest whatsoever in getting to know him. Brady was hurt by his father's cold dismissal. John was more interested in finding Mayor Marino's killer, since Sami was forced to go into the Witness Protection Program after witnessing the murder. He saved Marlena after she was attacked by the mayor's killer, but she was still frightened by his mercenary mode behavior and refused to be a part of his life unless he was willing to seek help.
John finally agreed to therapy with Dr. Charlotte Taylor, who was the daughter of Dr. Kenneth Taylor, Marlena's former mentor. The doctor seemed genuinely interested in helping John, but deep down held a serious grudge for Marlena. John appeared to like his new doctor, since she assured him that it was his decision if he didn't want to change his personality.
January 2009
John agreed to give hypnotherapy with Charlotte a try. She videotaped their session, and John remembered reuniting with Marlena on the pier back in 1991 after she was presumed dead for four years. Under hypnosis, John remembered her as the love of his life. John also remembered being chained up in a room with Marlena and insisted that she was in trouble and he had to help her. When Charlotte brought John out of his hypnotic state, he didn't remember anything. Charlotte lied to John and convinced him that hypnosis wouldn't work for him, so he quit therapy.
Marlena shared her suspicions with Brady about Charlotte's sudden defeatist attitude towards John. Charlotte tried to convince John to leave town with her, insisting that she could help him be a whole new man. Brady took it upon himself to break into Charlotte's office. He was stunned to realize that his dad was indeed getting his memory back. Brady emailed the videotape to Marlena, whose jaw dropped upon hearing John refer to her as the love of his life.
Charlotte soon discovered that someone broke into her office and was angry upon finding out that the videotape had been emailed to Marlena. She marched over to Marlena’s townhouse to confront her and taunted her with a hypodermic needle filled with a large dose of muscle relaxant. Marlena berated Charlotte for withholding information from John and for playing God with him. When John called Marlena to warn her about Charlotte, he knew Blondie was in danger and rushed over. Charlotte stabbed John in the back with the needle, causing him to collapse and suffer a seizure. John was rendered paralyzed from the neck down.
After Marlena reminded him of the love they shared together over the years, John finally regained his memories and remembered his love for Marlena. “I remember. I remember all of it Doc, especially you,” he whispered with tears in his eyes. However, Kayla gave the bad news that John had a catastrophic episode, and the drug which Charlotte administered to him destroyed part of his central nervous system. She predicted that if John stayed there at University Hospital even for one more day, his chances of recovery would be very slim. Kayla informed Marlena that there was a facility in Switzerland that specialized in these types of cases. John was devastated upon realizing that he was paralyzed and urged Marlena to walk away, but she refused to leave his side. John proposed to Marlena, and they had a beautiful bedside wedding before they left Salem for Switzerland on January 23.
