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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.