When HMAS Hammersley answers a distress call from Bright Island, Captain Mike Flynn and his crew discover a young woman lying paralysed on the beach. She is conscious but unable to talk, and despite their best efforts they are unable to save her. Thus begins new Executive Officer Lieutenant Kate McGregor's first day aboard a patrol boat, and CO Mike Flynn's obsession with the mystery of Bright Island. Something very odd is happening in connection with the Island. The Federal Police move in to investigate the woman's death, but no-one is talking. Her colleague, the striking Doctor Ursula Morrell, seems to know more than she's letting on, and Mike finds himself drawn to her cool beauty and her vulnerability.
The crew uncovers a people smuggling racket, when they almost collide with a floating shipping container full of North Korean refugees. The Hammersley races to capture the smugglers’ ship and save the lives of their human cargo. Kate is wooed by a charming civilian sailor. Meanwhile, Mike is determined to solve the mystery of Ursula’s disappearance.
The Hammersley saves sailors from a sinking ship, only to learn they are diamond smugglers who will kill to save their cargo. Swain is kidnapped by smugglers and left trapped in their sinking ship. Will Buffer rescue him before the ship sinks? Mike is reprimanded by Navy brass over his obsession with the Bright Island mystery.
The Hammersley races to save a boatload of tourists from being murdered as part of a bizarre terrorist publicity stunt. Meanwhile, Swain and the crew help deliver the baby of a runaway teenager, found lost at sea with her criminal boyfriend. A series of emergencies at sea prevent Swain from attending the birth of his first baby.
After the Hammersley successfully pulls off the tricky evacuation of all the Australian citizens from an island in the Samaru Archipelago, it comes across an FFV which isn't what it pretends to be. Charge discovers first-hand exactly how dangerous his job can be. And Nikki and ET have to decide what to do now that they're working together.
An ugly hostage situation on board HMAS Hammersley sees two of the ship's female officers taken hostage below decks. It’s a day of high tension, which begins when a group of shipwrecked illegal immigrants is rescued from a sand bay. Along with Afghan refugees, and a chronically ill Asian girl, are three super-fit Eastern Europeans who waste no time once they are safe on board.
The crew of the Hammersley are joined by a federal agent and go in search of an illegal fishing boat. Whilst on board the Navy find evidence on the boat and find the fishing boat crew start to exhibit symptoms of bird flu. One crew member faces a gruesome operation, while the federal agent learns that blackmail can work both ways.
Unresolved romantic tension has a dramatic effect on some of the Hammersley crew, after a savage mortar attack by insurgents on the Samaru island of Minatu. Mike and Jim are both critically injured during a bold rescue mission on Samaru. Meanwhile, Kate is made acting CO of the Hammersley. It’s up to Kate to handle a volatile beachside confrontation, and the medical evacuation of Mike.
Awaiting a call from his girlfriend, Buffer's attention is distracted by the Russian Special Forces tattoo on an aggressive passer by, which leads him to be inadvertently locked in a container on a suspect barge, heading upriver. Meanwhile, Commander Mike Flynn has recovered and is back in charge of the Hammersley, quickly reacting to a "mayday" call from the luxurious yacht owned by Ray Walsman.
The crew of Hammersley is rocked by the mysterious death of a much-loved shipmate. When valuable "Red Gold" coral is stolen from a dive boat, HMAS Hammersley is drawn into a web of murder, piracy and eco-terrorism. Then, Swain and Spider are kidnapped by an obsessed vigilante, determined to rid Australian waters of illegal fishing boats.
In episode three of Sea Patrol, the plight of a critically ill, pregnant woman presents a challenge to the medical skills and emotional stamina of several of the Hammersley crew. Yanlin (Hsiao Ling Tang) is one of a group of Asian women found when the patrol boat team boards a suspect fishing vessel.
Nikki starts investigating the mystery behind ET's death. But can she handle the truth? Swain risks his life to save a boy suffering from the bends. Spider tries to free a child slave from an illegal fishing boat, but lands himself in hot water. Tempers fray when Hammersley rescues an old enemy following a bizarre diving accident.
Hammersley is tasked with protecting a shipment of nuclear waste from a terrorist attack. When a bomb is discovered on board, Robert and 2 Dads must set aside their differences to save Hammersley. Buffer falls victim to a practical joke and Robert is tricked into going on a drunken date, with disastrous results.
Hammersley hunts down a mysterious gang of armed robbers, who are terrorising pearl luggers off the WA coast. Spider and Buffer have a trippy encounter with some hard-partying drug smugglers. 2Dads faces disciplinary action for negligence. Also, Mike is forced to intervene over rumours that Kate and Buffer are romantically involved.
Buffer gets a lesson in tough love from a sexy training officer. Hammersley is stranded in a deadly mine-field, after being attacked by heavy armed smugglers. Charge goes to extreme lengths to earn the respect of his estranged son and the crew are involved in a sailor's worst nightmare - fire at sea.
On patrol in protected waters in the Arafura Sea, a lazy comment from one Hammersley crew member to another that it's "about as routine as its gets" is the ironic curtain raiser to a day of horror. The crew of Hammersley launches a daring raid to recover a cargo of stolen uranium from armed terrorists. Kate queries Dutchy's professionalism after he injures her during a boarding party, and Mike's godson is taken hostage by smugglers.
Dutchy and Charge take drastic action to catch two prison escapees on a remote island. Hammersley rescues a kidnapped pilot with a dangerous secret. Charge finds himself in a psychological battle with a convicted murderer and Bird gets more than she bargained for when a routine operation turns nasty.
On patrol in the Arafura Sea, the Hammersley encounters an old adversary, an illegal foreign fishing vessel skippered by an infamous fisherman known as Hannibal. Robert is lost overboard in mysterious circumstances, sparking a major search and lives are at stake when Swain discovers rabies on board Hammersley.
There is something strange about the suspected foreign fishing vessel that a crew from Hammersley boards in the Timor Sea. On the deck are four Australian men who claim to be on a fishing trip, but Dutchy is suspicious of a fishing boat that seems to be carrying no bait, no nets, no fish and without any "blood and guts" on the deck. Further investigation reveals a cargo of illicit alcohol — and results in the XO being held hostage with a machete at her throat while the rest of her crew is sent packing.
The 'crash posting' of a Communications Technician to HMAS Hammersley proves to be a particularly nice surprise for one of her crew. However, 2Dads' suspicion of his old mate soon begins to grow, particularly when he suspects that Fraser is feeding vital intelligence to a group of pirates who have been ransacking boats. Mike and Kate use unorthodox tactics to catch the gang of daring pirates, .and Charge gets more than he bargained for when he finds love on a dating website.
A suicide bomb attack in a nightclub has a shocking impact on the crew of HMAS Hammersley. Dutchy goes undercover with the SAS to capture a group of deadly extremists before they can attack Australian targets. 2Dads risks his life to save Hammersley from a bomb attack. Kate's world is rocked when her former lover, SAS officer Jim Roth, returns to Hammersley. Mike risks his career by refusing to co-operate with a high ranking ASIO spy.
As part of the boarding party checking a possible FFV, Dutchy doesn't hide his surprise at seeing one of the crew is SAS Captain Jim Roth. His flash of recognition is noticed by the ship's master, and the question now is, has Jim's cover been blown? ASIO "spook" Madelaine Cruise is furious. She confirms that Jim was on a mission and insists CO Mike Flynn shadow the vessel in case Jim needs assistance. And so he does, after Dutchy sees two men fighting on the deck, and the subsequent boarding party finds an area awash with blood and Jim under a tarpaulin with a serious head wound.
2Dads and Charge come under fire while investigating a UFO sighting. Ryan and Bird befriend a young man with a tortured secret that could get them all killed. Charge hides a health scare that could end his navy career, and Mike suspects a local police chief of masterminding a major drug-smuggling operation.
Tragedy rocks HMAS Hammersley as the crew races to prevent a terrorist attack on a busy Australian port. Meanwhile, Kate and Dutchy discover ingredients for a radioactive 'dirty bomb' are being smuggled into Australia on illegal fishing boats, and Mike is stunned to realise SAS Officer Jim Roth has proposed to Kate - will he let the woman he loves marry another man?