Season 3

Sean's best friend is diagnosed with a progressive nerve disorder and lapses into a coma. Julia passes over Gosia for the new Nurse Manager and instead appoints the unpopular Eric Frost to the position. A professor of Jewish studies overdoses on his housekeeper's pills trying to induce vomiting after eating pork. His asthmatic housekeeper is then brought in after having run out of her medication. Evie and Sean end their relationship.

With growing opposition to Eric Frost as Nurse Manager, Julia reluctantly gives way and suggests to Gosia that the job could be hers if she could find a way to get Eric to leave on his own. Gosia springs in to action and Eric soon announces that he is quitting so that he can accept a ""better"" job at another hospital. Marina and Stella's medivac is used to smuggle drugs into the country.

Stella's brother comes into the ER suffering from a gunshot wound and, with assistance from Gosia and Arch, Stella tries to treat him covertly. When Julia discovers what is going on, she demands Stella inform the police. Stella places her career in jeopardy by refusing to turn in her brother but a good word on her behalf to Julia by Arch keeps her from losing her job. Stella and Marina disagree about the morality of putting a fourteen-year-old patient on the pill. Julia invites Tom to the track to watch her horse, Fine Young Hero, run. Evie is accepted into Pre-med

Sean brings in Ernie, a homeless man whose illness is exacerbated by his heavy drinking. A woman, brought to the hospital via medivac after her husband attacked her with a shovel, instigates a frantic search when she cuts off her finger in order to remove her wedding ring. While looking through old patient records for information on Ernie, Sean learns of Tom's illness

Ernie is readmitted to hospital with a dislocated shoulder and Sean is able to get him into a detox programme. Stella's treatment of a patient she believes to be a drug addict is questioned by Evie who asks for another doctor's opinion. A year after having left her order, Marina prepares for a visit by Monsignor Duval who is coming to determine her conviction. Julia has Arch ask Gosia to be ""nicer"" to the doctors. Arch extracts a man from a horse costume.

Tom and Arch bring in a cancer-ridden patient by medivac. Tom takes a special interest in the woman and wants her to receive whatever palliative care is available while Arch, recognising the hopelessness of her situation, tries to have her accept her imminent death so that she can help her children face what lies ahead. Tom takes out his frustration with the case on Sean who in turn lashes out at Ernie. Dave proposes to Marina, but feeling rushed and uncertain of her future, she says no. Arch stumbles upon Tom and Julia's now intimate relationship

Stella's brother is brought back to the ER with a stab wound and serious internal injuries after having been beaten. Ernie returns with a suspected broken ankle, and after he saves a patient's life using an advanced medical procedure, Julia discovers that he was once a doctor at Bethlehem West but left medicine after his wife was killed in a car accident. Sean and Evie are assigned to escort a transplant patient to the hospital but their ambulance gets into an accident in which Evie temporarily losses her sight—and Sean regains his confidence

Tom and Julia's medivac brings in a man who swallowed a fish hook on a drunken dare. Marina, Evie and Stella coax a quick recovery out of a young boy who is faking an illness so as not to have to go to church and confess his ""sins."" Tom collapses in the ER prompting the revelation of his illness to his co-workers. Sean's phobia surfaces when a young girl, along with her pet spider, is admitted. Arch is upset he was never told about Tom's condition and that Julia allowed him to continue to work in the ER.

Sean, Evie, and Gosia are called out on a medivac to treat a nine-year-old boy with a broken leg but instead find a group of homeless kids living in an underground sewer complex and a middle-aged man with an unknown illness. Returning to the hospital, Sean and Evie eventually diagnose the man as having an obscure 16th century sweating sickness and convince Arch to let them treat him with an equally obscure 16th century remedy. After their brief first encounter in a bar, Marina becomes a strange man's object of affection as he sends her flowers and begins to hang around the hospital. Tom refuses any cancer treatments that may prevent him from returning to work, but an unsympathetic Arch just wants him to be replaced.

After being called out on a medivac to an isolated farmhouse, Sean and Evie's pilot is murdered and their helicopter is stolen, leaving them to contend with the injured, and dangerous, partner of the man responsible. Marina continues to encounter her suitor, he conveniently appears to help her with a flat tire and then takes the opportunity to fix up her car. As Tom returns to work, Arch considers going to the medical board to have him placed on the impaired practitioners register.

Marina is surprised to discover that Mark Best, the strange man who's been pursuing her, has gotten a job as an orderly in the hospital. Responding to Marina's concerns about Mark's intentions, Arch steps in to confront Mark and tells him to stay away from Marina. However, to the bewilderment of Arch, when Marina hears Mark's side of the story, she begins to defend the behaviour of the man whom she once feared. When Tom collapses while working on a patient, Dr. Peter Michaels tells him that the time has come for him to leave his job. Stella informs Tom of a new experimental cancer trial that he may benefit from

When a gambling addict is brought into the ER following a failed suicide attempt, Evie encourages him to turn his life around, which he does, but only to have his hopes for the future dashed when he is diagnosed with terminal kidney failure that leaves him with less than a day to live. Marina is unsure about how to proceed with her budding relationship with Arch and resigns from her job for reasons of emotional turmoil. Julia and Tom are married.

Tom goes into cardiac arrest and is rushed to the hospital where he is revived by the staff. Dr. Michaels must quickly operate to relieve the increasing pressure the growing tumour is applying to Tom's heart. Having come through the surgery successfully, Tom begins his cancer treatments. Marina is unable to go through with her commitment to join a closed order and decides to give her relationship with Arch a second chance. Sean and Evie get back together and Evie learns she has received a scholarship that will allow her to study medicine full time