Auntie Joan is accidentally shot in her foot by Colonel Gilbert Spencer, who is excited about the rare birds nesting in the cliffs above her home.
Martin becomes concerned about patient Beth Sawle (Thelma Barlow) who has a fungal infection in her lungs and lives with her domineering and sinister sister Janet (Irene Sutcliffe), a biochemist who concocts potions and pills in a basement laboratory.
Auntie Joan, accompanied by her neighbour's dog Buddy, drops a pie off for Martin and suggests her friend Barbara (Georgie Glen) can help him with his fear of blood.
She applies for a job back at Portwenn Primary School, where her replacement headmaster Mr Strain (David Haig) is creating suspicion and public concern over his increasingly erratic behaviour.
Louisa later visits the elderly Mr Routledge (Ewan Hooper), to see if he will be vacating his unit soon, but Martin had previously denied his request to certify his physical needs as qualified to move to a nursing home.
Martin doesn't believe women are capable of balancing a job and raising children at the same time, and tries to discourage her, resulting in an ongoing feud between them.
Sally Tadwick (Sara Weymouth) the school secretary has just returned from a vacation in Spain and visits Martin to ask for medication to treat an infection from her new tattoo.
Dr. Edith Montgomery later recommends him to the very youthful therapist Dr Milligan (Paul Ready) to help Martin overcome his blood fear.
Dr. Martin Ellingham seeks out Louisa to talk about his new surgeon's job at Imperial College London, but they are interrupted by Bert Large, who wants to plan a baby shower for her.
Martin Ellingham's plans to resume his career as a consultant in London are put on hold following the birth of the (as yet, unnamed) son he fathered with his now estranged partner, Louisa Glasson.
He can't even afford the food and drink for a charity event to raise money for Florence Dingle's (Anne Reid) cat sanctuary.
Bert is also being chased by loan sharks Alastair Tonken (Alan Williams) and his son Norman (Marcus Cunningham) for the repayment of £1,000 they gave him to clear his debts, warning of repercussions if he doesn't pay up.
Unknown to Louisa, her mother Eleanor prefers to help Bert with his restaurant, so she drops baby James Henry off with teenager Angie Grappy (Angela Terence).
While Martin is tending Mrs. Dingley, Penhale hears Al, Bert and the loan sharks arguing, and orders the Tonkens to leave town and never return.
Mrs. Tishell discovers that she can no longer hide her infatuation with Dr. Ellingham and she decides that she must take drastic action, fuelled by a cocktail of drugs that are affecting her judgement.
With Louisa visiting her mother in Spain to get some perspective on their marriage, Martin knows he needs to try to change for the sake of their relationship, so he endeavours to keep his promise to her to see a therapist.
Aunt Ruth arranges an appointment for him with Dr Rachel Timoney (Emily Bevan), but a lifeboat training exercise causes problems for the doctor.
Louisa helps out her ex-boyfriend Danny when he brings seven children from London to camp on Ruth's farm – supervised by Al and Bert – while she and Martin plan a date at the suggestion of Dr Timoney.
Alexandra Lucas (Kerry Howard) has returned from India and attends the surgery; Martin diagnoses her as suffering from a highly infectious strain of hepatitis and tells her to isolate herself.
Martin later discovers Alexandra acting as the entertainer at James's pirate-themed first birthday party, generating a hepatitis scare that makes all the guests leave very quickly.
Threatened with arrest by PC Penhale if he continues his unlicensed whisky distillery Bert decides to go back to being a handyman, but that also has its drawbacks – his first customer is school teacher Erica.
What Dr. Ellingham's friends and family fail to realise is that he is actually trapped up at the Wilton farm, where desperate wife Annie is trying to coerce him into curing her seriously ill husband Jim.
Mature student Tina Collins (Samantha Spiro) is a classmate of Louisa's, giving her a lift to her classes, and has spoken to their lecturer about James' biting.
Penhale decides to have a police open house to raise community awareness, but local farmer Hannah Butler (Yolanda Kettle) arrives to file a complaint about theft of her sheep.
Hannah has orf (a viral skin disease which can spread to humans by handling infected sheep and goats) so cannot serve Al and Morwenna any food.
The rival captain, Alice Taylor (Pippa Nixon), has a problem with her leg, and Joe Penhale, acting as race umpire, sends her to see Martin; he diagnoses a Baker's Cyst and proposes to drain the fluid using a needle.
Morwenna persuades Al to take the place of one of the Portwenn rowers and Alice passes out again in the middle of the race, spurning Martin's offer of help when the boat reaches shore; it turns out that she has made a formal complaint about his treatment of her and his blood phobia.
American tourist Beth Traywick (Sigourney Weaver) returns to the village and asks Mrs. Tishell for help, trying to trace her distant Cornish relations as she fears she may have a hereditary illness.
Chris Parsons, who has given up drinking, is persuaded to try the Large's latest whisky, as a result of which he tries to kiss Louisa before experiencing a shaking fit; fortunately Martin arrives in time to give him appropriate medication.
Dr Rebecca Hedden (Hermione Gulliford), a representative from the medical council comes to assess Martin and his surgery and shadows him while he is seeing patients.