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. Personal lives aboard ship run amok. Second in command, Jenny Howard faces a crisis when her boyfriend asks her to move to New York just when Martin needs her most; engineer Andy is shocked to discover that his protégé Dave is the father of his daughter's new born baby, and a run on shore goes horribly wrong for ratings Mickey and Scouse.

With Operational Sea Training on the horizon Martin 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. Mickey is increasingly troubled by his failure of nerve in the trawler rescue. His unhappiness lands him in trouble both on Suffolk and on shore. Martin orders him off the ship to undergo psychiatric evaluation. Andy tries to cope with becoming a grandfather for the first time. He is worried about supporting Teresa and the baby, but also concerned whether they should accept Dave's involvement. Jenny makes the hardest decision of her life in turning down Alex's proposal. He leaves for New York without her.

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. Mickey is undergoing psychological assessments on shore, but still seems set on a path of self-destruction - until Rosie saves him from yet more trouble and he reveals the truth behind the trawler rescue. Freed of his burden Mickey successfully retakes the DRIU test and is allowed to return to Suffolk. Dave and Teresa's relationship moves up a gear when, much to Andy's horror, they agree to get married.

HMS Suffolk's weeks of hard work are put to the test in their final assessment, the Thursday War. But in the middle of one of the staged incidents, a real fire breaks out in one of the engine rooms. 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.