Shane came to Salem to keep an eye on Stefano DiMera's illegal dealings. He posed as Larry Welch's butler, and eventually learned of Stefano's acquisitions of two of three rare prisms designed by Larry's father. Shane teamed up with Bo, and the two intended on taking Stefano down. Later that year Shane learned that Stefano was about to acquire the 3rd and final prism through a Russian ice skating troop that came to town. Hope and Bo got the prism from the troop, but after a long chase with Stefano's men the prism ended up embedded in the ice rink. In 1985 Shane, along with Kimberly, Bo, and Hope, went to England to stop the Dragon, a terrorist who planned to kill Lady Joanna. Bo and Hope chased the Dragon, and managed to trap him in the Tower of London. Later the Dragon escaped, and made his way back to the US. Shane learned the Dragon was his old friend the Duke of Earl, and when he tried to kill Shane he fell to his death. Shane and Kim fell in love, and Kim began to experience attacks of temporary blindness. While in England they were shocked to find Shane's supposedly dead wife Emma alive. She had been brainwashed by the Dragon to kill Bo and Hope. Emma returned to Salem, and Kim backed away from a now married Shane. Later Shane and Emma divorced, and Kim and Shane reunited.

Shane bought what would become Donovan Manor, complete with the famous secret ISA room. Shane's ISA mentor and friend Levina "Peachie" Peach came to Salem and played the role of Shane's housekeeper. Shane and Peachie had been assigned a new case, they were to take Victor Kiriakis down. In 1985 Kimberly Brady came into the possession of a roll of film that contained some prints to the location of a treasure that Victor Kiriakis, and Stefano DiMera where after, which would again come into play years down the road. In Miami Bo, Hope, Kim, and Shane were all out to destroy Victor's plan. Shane had been imprisoned by Victor, but Kimberly slept with Victor in order to spare his life. Shane escaped, and managed free Bo and Hope who were trapped with an explosive that was meant to end their lives. Later Victor Kiriakis, Savannah Wilder, and Steve "Patch" Johnson were arrested for their parts in the crime syndicate in Salem. They were all freed when Victor blackmailed Larry Welch into taking the fall for everything. Victor knew Larry killed Megan, and used it against him. By the end of the year Shane and Kimberly became engaged, but Kimberly soon learned she was pregnant, and she feared Victor was the child's father. In 1986 Shane and Kimberly became engaged, but Kimberly hid the fact that she thought her child was Victor's. One day Shane heard Kimberly talking her about her fears and quickly broke off the engagement.

Later when tests where done to determine the father, Emma Donovan Marshall switched the results, and everyone believed Victor was the father. During a trip to West Virginia, in hopes of reuniting, Kimberly went into labor in a remote cabin in the woods. Shane delivered the baby, and he pledged his love for Kimberly and the child, and they planned to marry even though they believed Victor was Andrew's father. This news infuriated Emma, who tricked Kimberly into signing adoption papers. Emma took little Andrew and planned to sell him on the black market, but was eventually caught, and pleaded insanity and said she was still in love with Shane. However, Andrew wasn't found, and Shane and Kimberly split up. When Emma Donovan was found dead Kimberly was arrested and charged for the crime. Kimberly was innocent, and Shane worked to free her. Eventually Shane learned that Barbara Stewart had adopted Andrew from Emma. Barbara tried to flee town, but was killed when she crashed her car. Eventually Shane learned that his old partner Gillian Foster had killed Emma and set Kim up in hopes of ruining Shane and Kim's marriage. Andrew was returned to Kim and Shane, and the two reunited. On May 4 1987 Kim and Shane Donovan married. Later that year Andrew was hit by a car and rushed to the hospital. When a blood transplant was needed it was discovered that Victor could not possibly be Andrew's father, Shane was indeed his real father.

Shane's problems mounted when his old partner Gabrielle Pascal returned. Gabrielle pretended to be a Russian Spy who had an affair with Shane in exchange for secrets. When she let this evidence leak to the ISA Shane was fired. He was later reinstated after Emma was exposed. In 1987 Shane learned he had a daughter named Eve by Emma Donovan. Eve was a troubled young prostitute that Kimberly had befriended and eventually hired to watch over Andrew. Eve was out to break up her father's marriage to Kim because she blamed Kim for breaking up her parents, which she felt lead to her mothers death. Shane took Eve into his house, but she continued to be a problem for Kim, who was pregnant for the second time. Shane adopted Eve but she was soon forced back into prostitution by her old pimp Nick Corelli. Eve called Kimberly for help, and as a result Kimberly was attacked and lost her baby. Eve was also assaulted and a slash to her face from a knife left her with a permanent scar. Shane soon learned that Eve's mother was Gabriel Pascal, not Emma Donovan. An upset Kimberly left Salem to sort through her life. Shane began to have mixed feelings for Emma while Kimberly was gone, and even filed for divorce from Kimberly, who eventually returned to Salem.

When Shane's daughter Eve was attacked by the Riverfront Knifer, Kimberly decided to go undercover as a prostitute to catch him. Kimberly was attacked, and lost the child she was carrying. When Shane learned what Kim was doing he helped her, and as a result they reunited. Shane and Kim renewed their vows in 1988 and honeymooned in England. There Kim ran into a man she thought was Shane, only it turned out to be Shane's twin brother, Andrew "Drew" Donovan the III. Shane thought Drew was dead, but he had only been on a secret ISA mission. Drew returned to Salem with Shane and Kim, but Shane was suspicious of his brother. In the end it turned out that Drew was actually a crooked agent who was working for Stefano DiMera all along. In 1989 Shane accepted a dangerous ISA mission that sent him undercover. However Shane was double crossed by an old ISA friend Colonel Jericho, who abducted Shane and help him prisoner while the ISA and his family believed him to be dead. Shane eventually escaped and he and Jericho fought it out atop a mountain cliff, but when a bomb Jericho had planted went off they both went over the cliff. Shane lost his memory from the fall, but both Shane and Jericho were presumed dead once and for all.

In the mountains Shane, who had amnesia, stumbled upon Rebecca Downey. Rebecca had been on the run from her controlling husband and was camping out in the mountains outside of Salem. Unfortunately Rebecca's husband Arthur showed up and Rebecca got into a fight, both Rebecca and Shane thought Arthur was killed. Shane and Rebecca went on the run and told people they were man at wife. At a small Cabin they were staying at Rebecca found Shane's wallet which contained his real ISA badge, but she hid it from him. Rebecca wanted to use Shane to help her escape her husband plus she had fallen in love with him. Shane eventually found out the truth about who he was, but he still couldn't remember anything. Shane and Rebecca returned to Salem, and when Shane went home he found Kimberly making love to Cal Winters in his bedroom. Shane quickly left and he and Rebecca went to Chicago to try to clear Rebecca's name, not knowing that Arthur was still alive. After Rebecca was cleared, and Arthur was dealt with, Shane and Rebecca returned to Salem.

Cal plotted to have Shane killed, and when Rebecca opposed him he shot and killed her. Shane came home, only to be shot by his wife Kimberly. Kimberly thought Shane was an intruder because Cal had staged some phony break-ins and had given her a gun to protect herself, it was all part of his plan to have Kimberly kill Shane. Shane survived and in the hospital he learned that his wife had shot him. Shane forgave Kimberly, but another obstacle came in their way. Kimberly was pregnant, and she believed the baby was Cal's, not knowing Cal had blackmailed a doctor on staff to alter the baby's paternity tests. Kimberly tried to secretly have an abortion, but Shane learned about the baby and stopped her. The baby was too much, and Shane and Kimberly broke up. Kimberly left Salem and gave birth to baby Jeannie a few months later. When Kimberly returned to Salem, Cal Winters broke out of jail. Desperate to have Kimberly he kidnapped Kimberly, and her sister Kayla. Shane managed to save them both and Cal was taken into custody. Kimberly became suspicious about Jeannie and concocted a story that Jeannie had been hurt and she needed a blood transplant from her closest blood relative. Kimberly told this to Cal, and said that her blood type was different from Jeannie's so she couldn't donate the blood.

Cal broke down and told Kimberly that Shane was Jeannie's father. Shane bonded with Jeannie, but it wasn't enough to reunite Shane and Kimberly. Kimberly eventually left Salem and Shane plunged himself into his work. After Steve Johnson was murdered, Shane asked Kayla and baby Stephanie to move in with him. They grew close and bonded as they worked to find out who murdered Steve, who they suspected was murdered by Lawrence Alamain. Shane and Kayla grew closer and fell in love in 1991. Shane's old ISA partner, Peachie, returned to Salem to ask for Shane's help. Peachie had contracted a virus that was slowly killing ISA agents and she needed Shane's help. Once again, Lawrence Alamain was the prime suspect behind the deadly virus. Things got complicated when Kimberly returned to Salem and was partnered with Shane to investigate Lawrence. At a museum party in 1992, Shane's attempt to disarm a bomb planted by the Torres failed and he was left paralyzed. Shane refused to have surgery that could restore the use of his legs. Shane put up a wall that only Kayla Johnson could penetrate. Kayla helped Shane recover and the two realized that they had fallen in love. Shane eventually regained the use of his legs, but the tension between Kim and Kayla put a strain on his relationship with Kayla. Kayla eventually moved to Los Angeles to work in a clinic and Shane left Salem to return to England.

Shane returned to Salem briefly in the winter of 2002 when Hope was kidnapped by Larry Welch.

Shane returned in May 2010 when he was thrown in jail for trying to assassinate the leader of an island country. His cell mate was Rafe Hernandez. The two of them cooked up a plan to escape. Shane helped Rafe make his way back to Salem and then went back about his mission, but returned to Salem a few months later when he learned that Alice Horton was dying. While there, she reunited with her estranged husband, Shane and the two decided to leave town together and give their relationship another try.

Shane returned to Salem in 2012 to help out Roman with a secret operation where Rafe, Carrie, John, Marlena, Bo, and Hope faked their deaths to frame their murders on Stefano. After the case was over, Shane returned to California.

In the summer of 2013, Kimberly's daughter Jeannie, going by the name "Theresa", came to Salem. It was clear that Theresa and Kimberly had been fighting and Kimberly sent Theresa away in hopes that the rest of the family in Salem could get through to Theresa.

But the rest of the family was not successful. Theresa continued to do drugs and get into more trouble. One night, she overdosed and ended up in the hospital. Shane and Kimberly flew to Salem to see her. They wondered if leaving her in Salem was the best plan.

Kimberly and Theresa got into an argument about how Kimberly had been such a helicopter parent. Kimberly tried to make Theresa see that she only did so because she loved Theresa. Eventually, both women made up and Theresa promised that she would change, as long as she could stay in Salem. Shane and Kimberly agreed and said goodbye to their daughter.