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.
Kate is hunted down by an obsessed criminal after she kills his accomplice during a boarding. When Bird is kidnapped, the crew fears she will be murdered as payback.
Dutchy finds himself the prime suspect in a cold-blooded murder after he rescues a beautiful young woman. The Hammersley rushes to save a professional diver trapped in a shark cage.
Swain is obsessed with the mysterious sinking of a refugee boat. The crew uncovers a smuggling ring with a deadly method of sneaking goods into Australia, and Bird's romantic life is complicated when Mike's godson Ryan joins the crew of Hammersley.
Kate uncovers a deadly conspiracy when she investigates a cluster of rare illnesses on a remote island. Hammersley is on the hunt for a ship suspected of dumping toxic chemicals into tropical waters.
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.
Robert becomes the lifeline when 2Dads is trapped alone in a sunken research submarine. Mike and the crew pursue a marine biologist suspected of sabotaging the submarine, and with 2Dad's air supply running out, Charge must use all his technical skills to help save his mate's life.
Bird is compromised when she discovers Ryan working for a private security firm while AWOL from the navy. Mike fears his son has been murdered by mercenaries and risks his career to get revenge on the killers. A pregnancy scare forces Kate to reconsider her future.
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?