Thomas lies hospitalized in a coma, caught between life and death, after being shot; as his friends and family attempt to pull him out of the limbo in which he is trapped, Thomas has an out-of-body experience in which he sees himself in heaven, guided by Mac; Thomas recovers physically from the gunshot wound in time, but finds it hard to face life again; although three of the criminals who almost killed him are already dead, one is still free.

Still healing from his near-death ordeal and experiencing Mac's ghost, Thomas is surprised when Higgins hands over his estate duties to be able to take some time off; in a bizarre twist, Higgins starts living the fast and loose life, wears loud Hawaiian shirts and becomes irresponsible, while Thomas assumes Higgins' stuffy personality and ways, going so far as to wear a suit; curious about Higgins's sudden change in personality, Thomas investigates and discovers that Higgins is seeing a woman on the sly, and becomes concerned that she is taking Higgins for a ride.

Masters is sued by a man who tripped at a recent party on the estate; as Thomas begins to investigate the man, who seems to be a professional at making false claims, a loud-mouth businessman for whom T.C. is piloting pays Thomas to take his perky fiancée along on the case with him; when the man they're investigating is killed in a hit-and-run incident, they find themselves on an even bigger case involving a dangerous Mob figure; while Thomas's new partner means well, her over-eagerness doesn't exactly help matters.

Lieutenant Tanaka is murdered while working undercover. The official Police report states that Tanaka died in a car accident, but Thomas believes that something is being covered up, and sets about trying to answer the many questions about his friend Tanaka's death, uncovering switched identities and drug-running in the process...

Thomas is running an errand to a local museum for Higgins' upcoming pageant for the Anglo-Hawaiian Historical Society, when he catches sight of a woman attending a funeral who, he soon learns, resembles a beautiful Hawaiian princess who tragically died in a fire in 1910. Thomas becomes enamoured with the elusive beauty, and experiences visions of himself, in 1900s naval uniform, with the woman. The mystery grows even more when he receives a package in the mail containing such a naval uniform, and a locket holding photographs of what looks like himself and the princess... Is Magnum once again experiencing something ethereal, or is somebody using the story of the princess to their advantage?...

Thomas is trying to protect Carol, who is in the middle of a particularly controversial court case, when he is hired by a woman from the mainland to help locate the birth certificate for the child she gave up for adoption 30 years ago. But in doing so he becomes embroiled in Carol's personal life, as he discovers a powerful secret about her parents and her true birthright that could shatter her...

Magnum is hired by an attractive woman to find the missing will of her late father, who was recently killed in a suspicious boating accident - which she suspects her brother of being behind, in order to steal the will. Working on the case, Thomas finds that former client Susan Johnson – whom he was once locked in a bank vault with – is now a fellow Private Investigator, and is working on the same case – for the brother, who suspects his sister as responsible for their father's death. The two P.I.s are soon locked in a battle of wills as they both race to solve the investigation first, but the pair are forced to put their rather love-hate relationship to one side and team up to solve the case of sibling rivalry...

Magnum prepares for the trial of Quang Ki, who attempted to kill both him and his family. But when the case is suddenly, unexpectedly acquitted, angered Thomas suspects some other hand is behind Ki's release. It becomes evident that his arch-nemesis will stop at nothing to destroy Thomas and his family, when he receives a video-tape containing terrible information about the fate of his former wife and young daughter. As Thomas plans his revenge against Ki, he is thrust into a quagmire of intrigue endangering a sensitive P.O.W. prisoner exchange programme...

Higgins wants Magnum to find the ""Lost Art of the Ancients"", a priceless ancient scroll from a fallen civilization, that could spell disaster if it should ever fall into the wrong hands. But the search for the long-lost artefact is laced with abduction, danger and deceit, as an old flame of Magnum's, a foreign double agent, and a ruthless rival of Higgins' are all out to find the scroll as well, and the dangerous path to unearthing it could ultimately lead to death...

When Higgins asks his help in finding Robin's latest manuscript after it is stolen, Thomas gets some unexpected help in the case when St. Louis P.I. Luther Gillis arrives unannounced on vacation. They set about trying to work out who is so desperate to get hold of the manuscript that they are willing to resort to attempting to kill Higgins and drugging Zeus and Apollo to get it, in scenes reminiscent of those portrayed in the stolen book...

Thomas ponders his future while paying a visit to his family in Virginia, where he unexpectedly meets his grandfather and considers an offer to be reinstated to the Navy; Thomas returns to Hawaii to ascertain whether former girlfriend Linda Lee Ellison is being stalked; Rick prepares for his wedding to Cleo; Thomas and Linda renew their relationship as he searches for her stalker; Thomas becomes increasingly certain that his daughter Lily may still be alive.

As Rick's wedding looms ever closer, Thomas continues surveillance on Linda to catch the psychopathic killer who is stalking her; T.C. faces a reconciliation with his estranged wife; Thomas gets surprising news about his theory that Higgins is really Robin Masters, as well as the true fate of Lily.