An old flame from Arch's past provides Harry with legal advice regarding a doctor who knowingly exposed a patient to a fatal virus for the sake of performing a ground breaking trans-species organ transplant. Finally achieving the directorship that has eluded her, Julia asks Arch to accept the vacant position of Deputy Director—he refuses and then supports Wayne's bid for the job.

Danny Haywood, a man previously treated by Julia for severe depression (episode 8) is brought into the department under a police escort for treatment after going on a shooting rampage at a crowded public swimming pool. The grief stricken father of one of his victims accidentally shoots Peter while attempting to locate the gunman in the ER.

Gosia's abusive exhusband from Alice Springs shows up in the hospital looking for her. Repeat medivac flights to a farm lead doctors to suspect that the workers are intentionally electrocuting themselves in an attempt to cure their illnesses. Arch passes his fellowship exam and reluctantly accepts the Deputy Directorship. Wayne rebels against the practice of wearing helmets while on medivacs.

Bree and Gosia discover that Oopy is moonlighting at a private cosmetic surgery institute, Olympia's Secret, when a medivac returns with one of the institute's former patients who is now suffering from complications arising from her surgery. With the help of Peter, and his newly acquired pilot's license, Bree and Gosia take to the air to notify the institute's patients of the possible dangers associated with unnecessary cosmetic surgery. One of Arch's first official actions as the hospital's new Deputy Director results in a funding dispute between two charities

Harry is confronted by an old war buddy and his decision to tell the press about an off-duty killing they were involved in during their time in Vietnam. Instead, to clear their consciences, they personally fund the airlift of a New Guinean boy to the hospital for medical treatment. Julia and Gosia risk their lives to rescue the victim of a shark attack. Marina informs Julia about Oopy's other job.

After her rescue from the forest, a young school teacher tells of her abduction and subsequent impregnation by aliens. A skeptical Wayne believes her trauma is somehow related to her husband's recent death while Bree, unsure what to believe, just wants her to receive the help that she obviously needs. Soon after releasing the woman from hospital, Wayne and Arch are called out again to assist her after an apparent second abduction and are surprised to discover that she is no longer pregnant

Dr. Dexter Haben, still alive to the surprise of many in the department, makes an appearance to perform a life saving operation on an infant to garner some good press prior to his hearing on the trans-species organ transplant matter (episode 16). A suspected case of the equine virus threatens the life of Julia's young friend as well as those of her horses. A zoology student is brought in after having been scratched by a bat. Wayne is bitten by one of Julia's horses during a riding lesson

Harry is placed in the media spotlight following a fatal fire in a run down apartment building which he owns. Macy suffers from the ""say goodbye blues"" after treating a homeless man and getting to know his teenage daughter. Duelling celebrity impersonators are admitted to the department.

Medical practices in the ER are publicly condemned by hospital neurosurgeon Dr. David Delamere resulting in Arch being investigated on a charge of manslaughter relating to the death of one of his patients. No longer able to emotionally let go from her patients, Macy quits and takes a job in a nursing home. Monsignor Duval, a representative from the Vatican, arrives to investigate a potential miracle for which Wayne is the principle witness

The emergency department staff responds to the accident scene after a truck T-bones a bus full of blind school children. Arch's manslaughter trial begins, but he chooses to attend to the victims of the bus accident instead. Unable to stay away from the hospital after hearing about the collision on the news, Macy returns to help with the accident victims. Wayne and Gosia disagree on whether to inform the police about a young girl who was used as a drug mule. For failing to appear in court, Arch has his bail revoked and is remanded in custody

In the back of a police van en route to his trial, Arch comes to the aid of an aboriginal man who has a heart attack, the same man responsible for spearing an art dealer brought into the hospital earlier. Arch commandeers the van and redirects it to Bethlehem West making him late for his trial once again. Oopy's involvement in the mix up of two CT scans is uncovered by Bree and Gosia resulting in the charges against Arch being dropped.

After robbing Wayne's bank, a young couple are involved in a car accident in which the boy's head is pierced by a length of rebar. Emerging from surgery severly brain damaged, he is fataly shot by his girlfriend and partner-in-crime who is in turn shot and killed by Peter when she attempts to turn the gun on him and Marina. A paraplegic comes into the ER and overdoses himself into a coma, his wish is to have his organs sold to a dying billionaire to help support his family. His wish is eventually realised but Gosia sees that the payout is more appropriate for the magnitude of his sacrifice. Macy returns to her job as the emergency department's Nurse Manager. Bree fishes Harry out of the river and treats him for a jellyfish sting. Harry introduces the staff to the newest member of Bethlehem West's emergency department, Dr. Tom Shawcross

A medivac to a women's prison during a riot results in Wayne, Tom, and Macy being taken hostage by two inmates. Unable to simply fire Oopy, Julia tries to make him quit by assigning him to the supply closet. Nikki, a girl initially admitted suffering from burns to her arms, lapses into an unusual catatonic state that is broken by periodic outbursts of rage—her father believes she may be possessed. Harry tries to give Bree a gift to thank her for saving his life

The emergency department is quarantined when Nikki is believed to have a fatal rabbit virus. Dave Callen, Marina's medivac pilot, is blinded following an inflight explosion but Marina is able to successfully talk him through an emergency landing. Wayne attempts to sneak out of the hospital so that he can attend a stamp auction

Bree and Harry become intimately involved. A patient is attacked in the ER by the girlfriend of a man he killed in a car accident. After learning that he will be permanently blind in one eye, Dave tells Marina that he's in love with her. A discrepancy in the department's drug supply leads Julia to the discovery that Tom has cancer and has been taking morphine to ease the pain.

Tom forges the organ donation papers of a deceased patient whose mother is vehemently opposed to it, and then pays off the woman so that she won't sue the hospital. On a medivac to the site of a mining accident, Marina risks her life to go underground into the unstable mine in order to help a trapped man but can only watch helplessly as he dies before her. Marina allows herself to fall in love with Dave. Harry makes his relationship with Bree public

Wayne's 30th birthday lunch ends in a bout of food poisoning for the entire ER staff. The restaurant owner, a close friend of Julia's, tries to persuade her not to report the incident to the Department of Health and promises to take care of the problem herself. Madeline tells Arch she is pregnant but refuses his proposal of marriage. When a wealthy benefactor dies before signing a $330,000 check intended for a long awaited new x-ray machine, Tom forges the man's signature on the check to give him his ""bit of immortality."" Marina breaks her vow of celibacy by sleeping with Dave and then moves in with Arch when she leaves her order.

During an unusually quiet graveyard shift, Gosia personally welcomes new intern Sean Michaels to the hospital. In dramatic fashion, Oopy announces he is quitting to become a successful cosmetic surgeon in Hollywood. A light in an abandoned building across the street draws Wayne's attention, when he goes to investigate, he gets stuck in a malfunctioning elevator and then stumbles onto a computer being used in an illegal fund transfer of $80 billion from Swiss banks. Two twins treated after suffering nearly simultaneous heart attacks leave the hospital a sizable donation

Suffering from intense headaches, Arch sends Macy home to rest, but after passing out and crashing her car accident, Macy is admitted to hospital. Macy is initially believed to be okay and just in need of rest, but following a seizure it is discovered that she has a brain aneurysm. After asking Marina to give her last rights, just in case, the aneurysm bursts and despite the frantic efforts of her colleagues, Macy passes away. Bree and Harry are wed while Wayne, after a leave of absence from the ER, decides to leave emergency medicine entirely.