Although Kristen married Tony, she couldn’t stay away from John. She soon broke things off with John after finding evidence that he used to be a priest. John briefly lived his life as a priest before asking to be released from his vows. During his priesthood, however, he began to notice Marlena acting very strangely. It turns out that Marlena was possessed by the devil and even tried to kill John and Kristen. With the help of Father Francis, John performed an exorcism on Marlena and saved her. He and Kristen renewed their romance despite his strong feelings for Marlena.
Tony couldn’t bear Kristen leaving him for John, so during an extended trip to Aremid, he arranged to kill himself and frame John for his murder. As a result, John was sentenced to die in the gas chamber. Kristen began to have her doubts and turned against him. Marlena, however, believed in John’s innocence and stood by John the entire time. Just before John was sent to the gas chamber, he wrote a letter to Marlena which expressed his feelings of love for her. John was freed in the nick of time, but Stefano would soon capture John in Paris and sentence him to die by the guillotine. Fortunately, John was saved by his aunt Vivian.
Kristen caught on to John’s lingering feelings for Marlena and found the love letter. She went from a kind, loving person to a scheming witch who became obsessed with John. She soon discovered she was pregnant with John’s child, but lost the baby due to a gas explosion in Paris. She began wearing padding underneath her clothing to make it look as though she was pregnant and even used Stefano’s mind control device to get John to make love to her.
Stefano hired a Kristen lookalike in the form of Susan Banks to take Kristen’s place at examinations and childbirth. Shortly before giving birth, Susan posed as Kristen and married John in her hospital room. The baby was named John Jr. (who was later known as Elvis DiMera) and Kristen demanded for Susan to give him up. Susan actually developed a crush on John and locked Marlena and Kristen up in a secret room at the DiMera mansion before making love with John.
In the summer of 1997, John finally found out about Kristen’s lies and how she hired Susan to pose as her double. John married “Kristen,” but discovered the whole truth when Susan’s false teeth flew out of her mouth and into Vivian’s champagne. John and Marlena took pity on her and didn’t press any charges.
John and Marlena’s happiness was short lived, however, when Kristen brought a not so dead Roman back to Salem with an incurable disease he had received as a result of nuclear war. Marlena blamed herself since her affair with John years ago caused Roman to leave Salem and take on a dangerous mission. Stefano had the cure and took Kristen, John, and Hope to the jungle. They returned to Salem with the cure just in time to interrupt Marlena’s wedding to Roman.
Soon afterwards, Kristen was found dead in the pool at Peter Blake’s old house. Unbeknownst to everyone, the dead woman was actually Penelope Kent, Susan’s sister. Susan secretly arranged for Kristen to be shipped off to an evil kingdom.
John decided to continue to search for his past and went to Switzerland, where he discovered that he was a priest who shared a connection to Princess Gina. It was revealed that during Hope’s missing years, she impersonated Princess Gina.
John and Marlena were married on July 5, 1999. The happy couple honeymooned in Hawaii, where they spotted a drowning woman. John jumped in to save her but was shot with a tranquilizer gun and taken aboard a submarine. When he woke up, Hope, who was brainwashed as Princess Gina, transformed him into in her former lover John and they made passionate love. This was the beginning of the Baby Switch Storyline. John later washed up on shore, but had no recollection of the incident with “Gina” (Hope). Hope soon found out she was pregnant and tests confirmed that John was the father of her baby. In 2002, it was revealed that Bo was actually the father and everyone was overjoyed.
All of Salem was shocked when that same year “Tony” showed up alive and well at John and Marlena’s anniversary party. The truth eventually came out that Daphne DiMera was John’s biological mother, and that he and Tony were half-brothers.
In 2003, John had new troubling matters to deal with. Several beloved Salemites were killed off by the Salem Stalker. The evidence was pointing towards Marlena. John fought to prove her innocence and believed that Tony was behind the killings. John was devastated when his wife was arrested, then shot down by the police.
John would soon end up on the island of Melaswen, where he and others discovered the victims, including Marlena, alive and well. It turned out that Tony DiMera orchestrated the whole serial killing scheme and drugged and brainwashed Marlena into killing the beloved Salem residents. Tony held a serious grudge against John since his former wife Kristen left him for John years earlier. After a duel with John, Tony once again faked his death. When the residents attempted to escape the island, Tony caused a volcanic eruption which resulted in a tidal wave. John and others managed to escape on rafts, but he seriously injured his back in the process. Marlena, Roman, Cassie, Victor, Caroline, and Colin Murphy were among those presumed dead once again and were held captive by Tony in his European castle.
John was forced to move on without his beloved Doc and became addicted to pain medication, even acquiring it through illegal means. His good friend Kate Roberts helped him deal with his addiction. The two eventually fell in love and became intimately involved. Tony decided to torture his captives Roman and Marlena by forcing them to watch a surveillance video of John and Kate making love. Feeling heartbroken, Roman and Marlena found comfort in each other’s arms and made love. John and Kate were briefly engaged before Roman and Marlena finally escaped Tony’s clutches. John reunited with Marlena, while Kate reunited with Roman.
