The series resumes on a spectacular note with a helicopter crashing into an overcrowded pleasure boat. The fatality list is long but two survivors are trapped on the sinking craft unable to be moved.
While continuing to try to break out of the trap Charlie Driscoll has set for him, Jack finds himself caught in the middle of a power struggle taking place within Charlie Driscoll's crime empire.
A former lover of Alex's becomes a suspect in a murder investigation; and after Blakemore is forced to fire during an armed robbery, she finds her career on the line as Internal Affairs investigate.
Alex deals with the consequences of sleeping with Matthew Grierson, as the protest against the Marina development continues. Blakemore's career is in jeopardy when she is investigated by Internal Affairs.
ASIO enlists a couple of the Water Rats in a covert operation which causes Reilly to become the victim of an amorous spy and Sykes' love life gets him into very hot.
Alex and Reilly investigate the murder of a restaurateur for which their only witness is a ferocious dog. Sykes, Quinn, Woods and Rorke take part in an anti-terrorism training course.
Christey feels responsible when a grieving woman, who's brother was killed in an armed robbery, takes the law into her own hands and holds him and a suspect hostage.
The investigation of a murder yields the detectives two witnesses but each one identifies a different man as the killer. Meanwhile, Quinn and Sykes are kept busy by an elderly escape artist practising his dangerous craft in the harbour.
Alex is kept busy dealing with the problems of her fourteen-year-old sister, leaving Christey and Reilly to investigate a pair of robberies and two brutal murders.
Alex's undercover partner, and ex-lover comes back into her life after a series of death threats and she must take a hard look at the people she trusts.
A drug importing deal goes horribly wrong when a small time crim tries to implicate a notorious crime identity; and, a young woman appears claiming to be Christey's daughter.
Christey's week goes from bad to worse when he struggles with a major investigation and kidnapping and the discovery of a daughter he never knew he had.
Hawker becomes an unwitting accomplice to murder when he tries to help a friend; and, a young street kid becomes the prime suspect when his pregnant girlfriend is found murdered.
The Rats are caught off guard when they're ambushed on the harbour while transporting a wise-cracking prison inmate. When the getaway plans of the escapee and his girlfriend unravel, they take Christey and his daughter hostage.
As the resources of the Water Police are mobilised to try and locate Sophie, who has been bound and gagged, Jack goes off on his own to track down his daughter and her abductors.
When Constable Matthew Quinn takes the law into his own hands, he ends up in trouble with his girlfriend, local cops and Hawker; and, Christey, Alex and Reilly face quandary when they track a young woman on the run.
When a young man is shot dead in a boat shed, Christey's overzealous actions causes the boat shed floor to collapse sending the body and any evidence into the harbour.
A religious cult becomes the target of the detectives' investigation when the body of a murder victim is pulled from the harbour near their commune. Sykes searches for the woman who saved his life following a jet ski accident.
Convinced that a car accident was an attempt on her life, Alex investigates, only to discover a larger more frightening truth. Reilly and Christey come to blows over Alex.
Haunted by the brutal murder of a teenage girl, Alex puts her life on the line to identify the murderer; and Reilly wants to know where he stands with Alex.