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During a boarding to arrest 2 bank robbers, Dutchy is shot by a masked female accomplice and Kate kills her in self defense. The woman is later revealed to be Isabelle McGinley the younger sister of Heath McGinley, one of the robbers who managed to escape police custody with his partner. Kate then finds herself being terrorized by McGinley, who is trying to kill her to avenge his sister, first attacking her at NAVCOM and then when Dutchy went to her home to get some clothes, McGinley was already inside.

Meanwhile, Ryan White has just graduated from Naval College and invited Bird to a graduation party. While there, they and 2Dads are approached by a young man named Corey, who challenges them to a speedboat race, which ends in 2Dads being arrested while Corey escaped. Later that night, 2Dads is drugged and has his uniform and ID stolen, which is used by a mystery man to access the Navy Base and attack Kate, though he escapes from Dutchy and Mike.

The Hammersley crew boards an FFV, and finds four people murdered and a few terrified survivors, one of whom screams that they were attacked by the Australian navy. Kate starts throwing up for no apparent reason. Back at NAVCOM, Maxine White tells Mike and Kate that the evidence indicates that the FFV was attacked by the "Sassy," a boat owned by GD Security, a mercenary group run by a former SAS agent, Garth Davidson. Hammersley is tasked with intercepting the Sassy and bringing Garth Davidson back to port. Maxine privately asks Mike for his help in finding her AWOL son, Ryan. Boarding Sassy, the Hammersley crew discovers a large number of weapons and a foreign diplomat, Mr Tagobe. But Davidson has all the necessary paperwork for the armaments. Kate throws up again, but says she is fine. Meanwhile, Bird finds Ryan hiding below decks. Ryan claims he is out of the navy and in training with GD Security. He begs the reluctant Bird to keep his presence a secret. The Feds clear Davidson of the attack on the FFV. Kate consults Swain about her nausea; he offers her nausea medication and a pregnancy test. Mike goes with Dutchy to GD Security’s training centre to get Ryan. Maxine calls to tell Mike that Stewart White, Ryan's father, has succumbed to cancer. Ryan is insolent and dismissive when informed of Stewart White’s death, his own AWOL status, and that his upcoming mission with GD Security could cost him his life. Hammersley is ordered to escort Sassy, with Minister Tagobe and the diamonds he is carrying, back to international waters, and return the weapons. Swain arrests Ryan, but Maxine tells Mike that Ryan is no longer navy. Later, there is another mayday call from Davidson on Sassy. He claims to be under attack by pirates. When Hammersley arrives, they find five bodies, including Tagobe, but neither Ryan nor Davidson. Mike informs Maxine that it looks like Ryan is dead. Mike is determined to find out what happened and decides to go on a "goodwill" visit to Moroko, where there is a thriving diamond trade. They discover a known diamond trader and Davidson, very much alive, on his way to meet him. Mike confronts Davidson about Ryan. Davidson repeats his pirate story and tells Mike Ryan is dead and that he (Davidson) was the only survivor. Collecting evidence against Davidson, Mike sees someone he thinks is Ryan and chases him. It is not Ryan, but a young man named Jesus, who leads Mike to his injured son. Back on Hammersley, Ryan explains what actually happened, laying the blame for the deaths squarely on Davidson. A very happy Maxine tells Mike that Davidson was desperate to disappear because a video showing him ordering the massacre of Iraqi civilians has appeared on the internet. Hammersley finds the new boat on which Davidson and Sahid had left Moroko. Sahid has killed himself. Davidson thinks he has won, but Mike is furious, and, when Davidson starts a fight, he finishes it. Back on Hammersley, Davidson, certain that he is the only survivor, sticks to his story until he is confronted by Ryan, proving he is lying.

The Hammersley intercepts a vessel suspected of being used for human smuggling. The vessel is abandoned except for several very sick men and a Geiger counter. The sick men are determined to be dying of radiation poisoning and before dying one discloses that the boat had picked up two men carrying very heavy cases, which when covertly opened were found to contain metal rods later determined to be Cesium 137. Before being intercepted the vessel rendezvous with another boat and the two men transfer with the cases.

The Hammersley is dispatched to search for the boat with the cases. Prior to departure Jim Roth and Madelaine Cruise board; Jim takes Kate aside and proposes marriage. Kate says she’ll think about it. The Hammersley intercepts a fishing trawler which puts up heavy resistance; when boarded a quantity of Semtex is found leading to conclusion that terrorists are building “dirty” bombs for use on Australian soil. Using tracking data from the trawler’s GPS the Hammersley first travels to an island where another man is found dying of radiation poisoning, and then to a cruiser where a quantity of Cesium 137 if found. After a short, private interrogation of one of the prisoners Madelaine declares that all Cesium and Semtex has been seized and the threat is over.

Dutchy becomes suspicious of Madelaine’s behavior; Mike communicates his concerns with NAVCOM who dispatches all ships, including the Hammersley to search all ships approaching Australian ports. The Hammersley intercepts a cruiser heading for Cairns harbor and a fully assembled dirty bomb is found. Madelaine is caught phoning an unknown party reporting the interception. Jim volunteers to try to disarm the bomb; Swain to pilot the cruiser to open water and the rest of the crew returns to the Hammersley. Jim and Swain manage to separate the Cesium from the bomb and throw it overboard; the Semtex explodes killing Jim and Swain.

In a moment of truth before a posthumous award ceremony for Jim and Swain, Kate tells Mike she went shopping for a wedding dress but realized that there was only one man she could marry. Mike replies that there’s only one woman he could ever marry.

• Season 1
• Season 2
• Season 3
• Season 4
• Season 5

• Mike Flynn
• Chris Blake
• Rebecca Brown
• Leo Kosov-Meyer
• Dylan Mulholland
• Josh Holiday
• Nikki Caetano
• Pete Tomaszewski