John and Marlena eventually married in 1999, but on their honeymoon, John disappeared and was brainwashed by Stefano into sleeping with Hope Williams Brady. Hope found out soon after that she was pregnant, and John was believed to be baby Zack's father, until it was proven the father was Hope's husband, Bo. When a serial killer called the "Salem Stalker" began to murder Salem's most prominent citizens, evidence suggested that Marlena was the stalker. She was caught and sent to prison, but John worked to prove that Marlena had been set up. Marlena ended up shot by the police while trying to escape, and died in John's arms. John eventually uncovered that the Salem Stalker debacle was another diabolical DiMera plot; Marlena and her "victims" were found alive on a remote island, "Melaswen" (New Salem spelled backwards). John was seriously injured during his failed rescue attempt. Addicted to painkillers, John sought solace in the all-too-welcoming arms of—and proposed to—Roman's widow Kate Roberts. John and Kate eventually broke off their engagement when Roman and Marlena managed to escape Melaswen and reappeared in Salem. When Marlena became an amnesiac, the specialist summoned to help her – Dr. Alex North – turned out to be her first husband, presumed dead, making Marlena's marriage to John invalid. Marlena rejected John's love, feeling obligated to Alex. Nevertheless, John discovered that Alex was a fraud who had plotted to marry, then kill Marlena. He was able to save Marlena, who eventually got her memory back.