Sam leaps into various points, over a six year period, in the life of Lee Harvey Oswald (Willie Garson) in an effort to seemingly prevent him from killing President John F. Kennedy or find the truth about the events that day. However, the objective is made more complex by the fact that their minds are merging. Sam starts to believe he is Oswald. During his leaps whenever Oswald's mind is ascendant, he lashes out at wife Marina Oswald (Natasha Pavlovich), girlfriend Mariska (Donna Magnani) and his training leader, Sgt. Lopez (Reni Santoni). He then attempts to defect to Russia and divulge classified US military information.

Sam finds his patience tested when he leaps into Nikos Stathatos (Socrates Alafouzos) in a lifeboat with a bratty, self-obsessed heiress Vanessa Foster (Brooke Shields) and end up stuck on an island from which they will not be rescued for nine years.

Sam leaps into Ronald Miller (Michael Carpenter), a legless Vietnam vet in a veterans' hospital who must save the life of Billy Johnson (Michael Boatman), his quadriplegic roommate, while still keeping his host's wife, Julie (Judith Hoag), from leaving him so that his eldest son can save a tank troop in the Gulf War. All the while, Sam is touched by the kindness and sadness of Kiki (Jennifer Aniston), a hospital volunteer whose brother is missing in action.

Sam leaps into Leon Stiles (Cameron Dye), a dangerous criminal who has taken Carol Pruitt (Connie Ray) and her young daughter, Becky (Beverley Mitchell), hostage. Meanwhile, Al must find the homicidal Stiles, who has escaped from the project waiting room, leaving Gooshie to act as a temporary Observer.

Sam leaps back into Jimmy LaMotta (Brad Silverman), but is perplexed when he finds that the happy future he supposedly ensured in his previous leap is not taking place, and the marriage of his brother and sister-in-law, Frank (John D'Aquino) and Connie (Laura Harrington), is falling apart. Shortly thereafter, Sam finds something he never expected. A female quantum leaper named Alia (Renée Coleman), aided by observer Zoey (Carolyn Seymour), is apparently there to "put wrong what once went right".

Sam leaps into a small Louisiana town as a sheriff named Clayton Fuller (James Whitmore Jr.) who's also the father of 10 year old Abigail Fuller (Kimberly Cullum), a girl accused by local townswoman Leta Aider (Mary Gordon Murray) of killing her husband and daughter, even though the daughter was never found and the town doctor (Max Wright) confirms the husband had a heart attack. Leta believes Abigail to be cursed, as mother Laura Fuller (Meg Foster) is in an asylum, with Abigail cared for by Fuller family housekeeper Marie (Fran Bennett). Deputy sheriff Bo (Stephen Lee) and the doctor's son, Will (Travis Fine), both help protect Abigail from Leta's attacks, though Sam must save his host and Abagail from dying in a house fire.

Sam leaps into Larry Stanton III (W.K. Stratton), a lawyer hired by Marie (Fran Bennett) to defend Abigail (Melora Hardin), on trial for the murder of Leta Aider, the woman who got away with killing Abigail's father (Sam's then host) after she accused Abigail of killing her husband and daughter twenty-three years earlier. Abigail's marriage to Will never took place, though she has a daughter, Samantha Jo Fuller (Kimberly Cullum, who played young Abigail in Part I), from the night with Sam, as Will, 11 years earlier. When Sam visits Abigail's mother Laura (Meg Foster) at the asylum, she again recognizes him from his two previous visits, as two other hosts. Secrets are revealed, the family history comes unraveled, and surprises are in store for Sam as he discovers the heritage behind Samantha Jo.

Sam leaps into his hometown as Willie Walters (Daniel Engstrom), one of three brothers who are robbing the town bank in order to pay off a loan. Sam must uncover the reason the bank lent money to these farmers who could not possibly pay it back, while trying to prevent the brothers from being killed when they try to escape.

Note: Scott Bakula plays a dual role in this episode, also appearing as Sam's father, John Beckett.

Sam leaps into the famous sex doctor Ruth Westheimer (played by herself), in the middle of her radio call-in show. Sam must help Annie (Robyn Lively), one of her callers, stand up to the sexual harassment of her boss, Jonathan (James McDonnell). The situation escalates, with Sam having to stop Jonathan from raping Annie. Sam also carries out his original mission, getting Dr. Ruth's radio coworkers, Doug (Peter Spears) and Debbie (Anita Barone), into a lasting relationship. Back in the PQL's waiting room, Dr. Ruth helps Al deal with his fear of abandonment (raised in an orphanage, divorced by Beth) and his inability to tell Tina that he loves her.

Sam leaps into an eccentric artist named Lord Nigel Corrington who lives a strange, Gothic lifestyle. He must deal with Al's conviction that Sam's host is a hundreds-year-old vampire, while trying to keep Corrington's potentially walking dead acolytes, Victor (Ian Buchanan) and Claudia (Deborah Moore), from killing his host's new wife, Alexandra (Shae D'lyn), as a blood sacrifice.

As nerdy college kid Arnold Watkins (Tristan Tait), who dresses up as a superhero, Sam must stop Mike Hammond (Neil Patrick Harris) from operating dangerous chicken races as part of his fraternity's initiation ritual. In the PQL waiting room, Al must convince Sam's host to give up his dangerous lifestyle and help him deal with witnessing the murder of his parents. However, the sudden return of Evil Leaper Alia (Renée Coleman), and her observer Zoey (Carolyn Seymour), makes the task significantly harder.

Leaping into Elizabeth Tate (Cynthia Steele) in a women's prison, accompanied by former Evil Leaper Alia (Renée Coleman), who has leapt into fellow inmate Angel Jensen. With Alia having been extracted from the evil project, former observer Zoey (Carolyn Seymour), who is the new Evil Leaper, accompanied by new observer Thames (Hinton Battle), leaps into the prison's warden (Sam Scarber), as Alia had been traced there before contact was lost. Sam must help Alia escape all contact with the evil project, while keeping his host from being falsely executed for the murder of a fellow inmate. With help from honest guard Vivian (Barbara Montgomery), to whom Sam reveals the truth of his and Alia's situation, Alia is able to escape for good.

Note: Set in 1987, this is the most advanced date of any leap shown during the series.

As Elvis Presley (played by Michael St. Gerard), Sam must help a struggling female musician named Sue Anne Winters (played by Mary Elizabeth McGlynn), but at the same time must ensure that he does not prevent the king of rock 'n' roll from being discovered.

Guest star: Gregory Itzin

In the series finale, Sam arrives at a mining town as himself on the date and exact hour he was born. Patrons of the town bar look familiar from past leaps, but with different names, while one (W. Morgan Sheppard) even has the same name and bad breath as Gooshie – but has a reflection revealing to Sam that he is also a leaper. Al the bartender (Bruce McGill) takes everything in his stride, even when Stawpah (Stephen McHattie), who helps Sam save two miners, leaps out without leaving a host behind, and is only remembered by him and Sam. Sam theorizes that the bartender might be God. Al the bartender denies being God, then tells Sam that he controls his own leaps and could return home whenever he wants. Al Calavicci eventually locates Sam, but is unable to shed any light on the situation. He does, however, confirm that Stawpah is a figure from his own past. As much as he wants to go home, Sam decides to revisit Al's wife, Beth (Susan Diol), and tell her that Al is still alive. Al and his wife remain together and have four daughters, while Sam never returns home.