One year after Al and Morwenna?s wedding, the doc is mending old clocks and getting underfoot, caring for the new baby, Mary Elizabeth, and Louisa is using the surgery for child counselling. Mrs. Tishell tries to convince the doc to go back to work, asking for signatures and stapling her hand. Penhale does his best to issue formal warnings to keep the Doc away from a woman who is constantly tired and winds up in a car crash. Ruth goes to a serial killer?s convention. Morwenna tries to convince Bert and Al to jointly take over an abandoned caravan park in order to impress her boss at her new job at the local estate agent's. The doc finally realises he wants his job back and admits his mistakes to ultimately get it back.

The realisation that things are getting a bit cramped, with both Martin and Louisa working out of the surgery, sees the two explore new premises, in the form of a house on the other side of town being sold by George Upton, recently widowed, and who has been the victim of noise complaints over recent nights and?? what Penhale assumes?? possible supernatural interference. Al and Bert's attempts to get their caravan site up-and-running are plagued by difficulties, including Al accidentally being stabbed by his food van colleague, and a worker hired to clear out fly-tipped rubbish continually on the verge of passing out. Morwenna's concern for George winds up with her being enlisted back into her old receptionist job, when the surgery becomes as dysfunctional and chaotic as the new temp, Max.

The doc encounters park ranger Stewart James on a home visit to a local farmer, and invites him for a long-awaited check-up, where Morwenna coerces Al and Joe into attending one of his survival courses, which Stewart is becoming stressed over ensuring the success of, and Al is reluctant based on Stewart's past mental health problems. Stewart's mental state seems to deteriorate as the evening goes on, and Al manages to escape and enlist the doc?? who uncovers a link between Stewart's delusions and the local farmer's ailments as he attempts to sell off sheepskins. Pippa, the new headteacher at the local school, is enthusiastic over the?? albeit unsanctioned?? garden she has set up, when she develops a rash, and her health suddenly declines at an event at the school when learning many of the children have also.

The doc faces multiple patients whose ailments have been exacerbated based on the advice of a herbalist that has set up shop in the village, and discovers the link between her opposition to modern medicine and a supposed young mother whose baby shows the signs of mumps. Mrs. Tishell is determined to help Irene Moore get back in the water after she is told to avoid her usual morning swim in case it flares up her ongoing migraine issues. An old flame of Martin's from university turns up inviting him to a conference, to Louisa's displeasure?? who is already dealing with James' jealousy over the attention baby Mary is receiving. Ruth's return from Mexico sees some attention from Chicken, the family's adopted dog, and the revelation she has developed deep vein thrombosis. Joe deals with guilt over believing he has accidentally poisoned former fianc?e Janice in an attempt to woo her back over dinner, when it becomes clear the blame rests with her new fish pedicure sideline.

Louisa receives a shock when her father Terry turns up at the house, with both her and Martin suspicious of his intentions, having just been released from prison; he confidentially discloses to Martin that it was on compassionate grounds, having been diagnosed with terminal motor neurone disease, although Martin is not convinced that diagnosis is accurate. Meanwhile, he deals with the two squabbling siblings who own the fish shop, in particular why one of them appears to have continuous sea sickness on land, and Ruth's attempts to further help him progress on tackling his blood phobia by leaving it in various forms in numerous places around the surgery, designed to see how he copes with unexpected appearances of it. Al is less than impressed with Bert when he reveals his plans to return to the whiskey distilling business, and his efforts to expel a squatter from a caravan he's trying to sell. Joe tries to act hard to get around Janice.

Martin jets off to London to make the keynote speech at a conference he's been invited to, attending to a member of an injured bridal party on the way over, and the behaviour of his ex-girlfriend Sophie. Janice calls upon Joe for help while babysitting for James and Mary.

All of Portwenn is gossiping about Martin?s Imperial College job offer, but he is as of yet indecisive. Caitlin blames Bert for flooding the pub?s cellar, and an emergency on the rocks with Chris Parsons helps Morwenna make a crucial decision.

It's Louisa and Martin's last day in Portwenn and, when Chicken the family dog goes missing, James refuses to leave without him. Martin and Louisa go to look for Chicken at Martin's late aunt Joan's old farm when the new owner reports he's seen the dog there. They find the dog, but cause a cattle stampede. Martin has a serious accident on a barbed wire fence and is seriously injured. There's no cell signal, so Louisa must fix his wound as best she can and take him to the hospital. When Mrs. Tishell finds the surgery completely empty, she "loses the plot". Martin recovers and he and Louisa decide to remain in Portwenn.

Christmas arrives and Doc Martin and Louisa take James to see Santa, portrayed by Leonard (Ron Cook) . Martin notices Leonard scratching a rash and closes the grotto, concerned that he may be contagious. Martin hears that his mother has died of a heart attack. Mrs. Tishell, believing that she may have throat cancer, kisses Martin under the mistletoe in her pharmacy, and he storms out in anger, but later returns, discovers she only has GERD, and, incidentally, no longer needs her neck brace. Some "psycho" (Joe Penhale) is leaving birds (three hens, two doves) in Janice's shop (after she tells him her favorite song is "The Twelve Days of Christmas"), which is terrifying her. Louisa works hard to organize a Christmas lantern parade like the ones she remembers from her childhood. On his way to visit Leonard after hearing over the phone that he had seriously cut his leg, Martin crashes his car in the snow and trips over and falls unconscious. He wakes up two hours later, suffering the effects of hypothermia. He hallucinates that he sees his mother, though manages to contact Louisa to relay his situation and makes his way to Leonard's farmhouse. After recovering, Martin concludes Leonard has Coeliac Disease based on the rash along with other symptoms and Leonard isn't contagious as a result. After tending to Leonard's cut leg they take Leonard's sleigh into Portwenn, and Martin takes James for a ride. Morwenna tells Al that she is pregnant. Joe Penhale proposes to Janice and she accepts.