Morale is flagging and standards have slipped aboard HMS Suffolk. New Captain Martin Brooke finds himself thrown in at the deep end; he and his fractious crew are fast approaching Operational Sea Training, the toughest test of their careers, and time is running out. Unfortunately, things don't run as planned on Martin's first day at sea. Suffolk becomes embroiled in the frantic rescue of a trawler full of illegal immigrants stranded in the busy shipping lanes.

With Operational Sea Training on the horizon, Brooke puts the Ship's Company through its paces in an intensive few days of Harbour training. His aims are compromised by the unexpected arrival of an Argentine Naval delegation.

Suffolk runs into trouble at sea attempting to help a group of environmental activists, protesting against the shipment of nuclear waste. Things get heated aboard the activists' boat after a fracas between Buffer and a crewmember. Shockwaves are felt throughout the Royal Navy when the press take up the story. As a result, Buffer faces losing his career.

Weeks of hard work are put to the test in their final assessment, the Thursday War. But in the midst of one of the staged incidents, a real fire breaks out in an engine room. Lewis is forced to act quickly to save the ship but his decisions have fatal consequences. Teresa's extravagant spending finally catches up with her. Sam and Anita embark on a dangerously clandestine cross-ranks affair.

HMS Suffolk comes to terms with the aftermath of the Thursday War, as Lewis is initially cleared of responsibility for Andy's death, only for Martin and Jenny's further investigations to cast doubt on this verdict. Dave and Teresa are reunited and the wedding is back on, while Sam and Anita's illicit affair hots up.