Mrs. Carolyn Muir rents charming Maine Gull Cottage for her family and finds that it comes with a resident ghost. Captain Gregg takes a shine to the pretty widow and allows them to stay in his house.
After an appeal to the vanity of their landlord doesn't work to get needed repairs made, the Captain sends him on a treasure hunt in the very areas that require fixing.
Unknown to Mrs. Muir, she gives access to Gull Cottage to a ghost hunter looking for the spook that inhabits it. When she learns her mistake and orders him out, the ghost hunter turns nasty.
The local historical society wants to erect a statue of legendary local Navy hero Captain Figg. Captain Gregg is insulted that he wasn't chosen and wants Mrs. Muir to expose Figg as the coward he was, but Mrs. Muir must have proof.
Vanessa Peekskill, the great-great-granddaughter of Captain Gregg's true love, comes to Gull Cottage to research their romance, and the Captain is quite taken with her.
Claymore switches the Captain's antique barometer with a fake and sells it to some antique hounds. Captain Gregg switches them back and Claymore is arrested for fraud.
Mrs. Muir's Uncle Arnold who sells magic tricks comes for a visit. Candy asks for him to stay and perform at her birthday party until they find his tricks don't work and his stories grow old and stale fast.
Captain Gregg reluctantly consents to removal of the antiques and replacing them with modern furniture to make the cottage a home, but when she has his prized monkey puzzle tree cut down after a window is broken the angry Captain leaves.
Mrs. Muir needs money to fix the plumbing and can't come up with a single idea for an article, so the Captain collaborates with her on a story, but his secret revisions start giving people the wrong idea about her.
Prompted by her family doctor, Carolyn sees a psychiatrist, who convinces her that the Captain is a delusion she should ignore. When the psychiatrist shows up at Gull Cottage, the Captain takes delusion into his own hands.
When Jonathan accidentally tells Carolyn's visiting in-laws about the Captain, they believe he's a living person and jump to the conclusion that Carolyn plans on marrying him.
The Captain's attempt to make up for interfering in Jonathan's education involves scrimshaw, a parasol, a loan from Claymore, and a lot of regrettable secrecy.
Taking a job at the Schooner Bay Beacon, Carolyn finds herself overworked by the editor. The Captain misses her, and has never forgiven the Beacon's inaccurate reporting of his death.
Jonathan's history essay wins first place, but when he changes the essay to reflect facts the Captain provides, he stirs up resentment and puts his prize and the family's peace in jeopardy.
Carolyn comes down with a bug, and Captain Gregg, dissatisfied with the doctor, concocts his own remedy which sends Mrs. Muir back to the mid-1800's where she is the "ghost" and the very much alive Captain is the only one who can see her.
The Captain is continually interrupted when trying to read Carolyn his poem for her, but her rapt attention to a singer-songwriter stranded at Gull Cottage gives the Captain an idea for getting his poem heard.
