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.

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.

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.

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.

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.

After going on a blind date with an SAS commander, Kate believes her love life is starting to look up. When a French naval captain attempts to seduce Mike, he has to call on all his diplomacy skills. An illegal fishing boat is the subject of a perilous boarding.

Robert fails a drug test but is determined to prove his innocence. Meanwhile, the Hammersley uncovers a smuggling operation by Samaruian rebels which is designed to destabilise the government.

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.

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.

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.

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.

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.

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.