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 Hammersley uncovers a sophisticated drug smuggling network, with explosive results. Mike is convinced the Federal Police are covering up the poisoning death of a marine biologist. Kate is jealous of Mike's relationship with Ursula Morrell, while Nikki struggles to restrain her feelings for ET.

The crew of the HMAS Hammersley come across an abondonned catamaran in the middle of the ocean, which uncovers the beginnings of a murder mystery. A sailor has gone missing and Nikki puts her navigational sklls to the test in the attempt to find them. The ship is then hit by a cyclone.

Mike is torn between saving the life of a missing refugee girl, and the lives of two shipmates bitten by the deadly irukandji jellyfish. While pursuing pirates, the Hammersley rescues a family of illegal immigrants from an unseaworthy ship.

The Hammersley attempts the daring capture of an illegal fishing ‘mother ship’ but is thwarted by violent eco-terrorists. Mike finds himself falling in love with beautiful marine biologist Ursula Morrell, who later goes missing under mysterious circumstances.

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 HMAS Hammersley confronts a series of new menaces in the northern waters from pirates to toxic crabs, not to mention a gorgeous solo yachtswomen with a rescue fetish.

The video of Chefo's bucks night finds its way into Kate's hands and she is humiliated by what she finds on it. The HMAS Hammersley comes across an unexploded sea mine and Spider manages to save the life of a boy who was near the mine, but have Spider's days in the navy come to an end?

Disaster looms for the Hammersley crew when a fire erupts in the engine room, after the mascot is stolen by a rival Patrol Boat crew. Meanwhile, an eye injury threatens to destroy Charge's career, and ET takes a vow of chastity in a desperate attempt to prove himself to Nikki.

The crew pursues a distraught father who has kidnapped his own children. Then, while searching a crocodile-infested swamp for the missing family, the crew discovers a badly mauled fisherman.

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.

As the decommissioning of the HMAS Hammersley draws near, the crew risks life and ship to hunt down a rogue terrorist boat and retrieve its cargo of bio-toxins. In ordering the sinking of the rogue ship, Mike makes the most difficult decision of his career.

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.

Despite being determined to earn respect, Hammersley's new chef "Bomber" Brown but faces discipline after losing her temper with another crew member. Also, the crew discover a dead pirate and a killer cargo on board a stolen boat.

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.

The crew find a boy who has found a cache of guns. The boy is later kidnapped which ends up ruining a date for Kate and Jim. Meanwhile, one crew member faces losing the love of his life.

Bomber Brown and Spider Webb fall overboard and as the man of the watch, Buffer takes it hard that the two missing officers might drown. Meanwhile Buffer also deals with a personal tragedy.

The Hammersley is once again in hot pursuit of the cabin cruiser responsible for trafficking weapons and ammunition to the Samaru Islands. Meanwhile Mike Flynn receives a tempting offer from Ray Walsman and Kate's life is placed in danger when she becomes isolated from the crew.

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.

A change of command on HMAS Hammersley results in divided loyalties and the humiliation of the ship's most senior female officer. After a dangerous departure from Samaru, Commander Mike Flynn is recovering in hospital.

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.

Buffer becomes a marked man after providing evidence allowing the Hammersley team to arrest Ray Walsman, and among a team of UN observers later taken on board, is one man with murderous intent. Walsman meanwhile has escaped, but a quick thinking Mike has him back in custody.

The crew of HMAS Hammersley uncovers a terrorist plot to assassinate a senior US official. Kate has doubts about Hammersley's popular new crewmate, a war hero with a dark secret. Mike resists a promotion to Navcom, even though it would allow him and Kate to pursue their relationship.