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22 Episodes 1998 - 1999
Episode 1
When a homicide investigation into the disappearance of a teenager babysitter fails to reveal any useful evidence, Church and Angie go undercover to infiltrate a sinister criminal family. The Unit is faced with a race against time to prevent the killer from striking again.

Episode 2
When Undercover learns that well known criminal Travis Winter is the go-between in the hiring of a hitman, Church goes undercover as a gun-for-hire. Winters' client is Fleur Newstead and the target is her husband, Roger Newstead. Fleur claims her husband is trying to kill her, and she wants to get him before he gets her. When events take a sudden turn for the worse, the case is handed to Homicide, and Church is taken off the job. Against orders, Church goes out on his own to solve the case.

Episode 3
When a police officer is shot, the Stingers unit is sent to investigate the prime suspects within the Romanian gang. To assist the team, Rocca calls in Nick Torris, an ex-undercover operative of Romanian decent. Nick resents being forced to go undercover again, even with Kaye by his side posing as his girlfriend, and has fears about the operation.
Episode 4
When a serial killer takes a third victim, Undercover is called to find the killer before he tries again. Angie goes undercover as bait with Church and Stone in support. The Unit turns up several suspects but nothing that brings them closer to the killer. As the pressure builds, Angie's cover is blown and Kaye must go in as her replacement. It is Kaye's first job and the Unit moniter her progress carefully. Kaye is working well, when all of a sudden contact is lost and Kaye vanishes.

Episode 5
The Unit goes into damage control following Kaye's disappearance, scrutinising the surveillance footage and following up the few leads they have a process that provides an unexpected lead. When Rocca informs Hollister the killer is possibly a member of the force, Hollister hauls the suspects in for questioning. Angie and Stone search for the evidence they need to make a conviction, but a horrific discovery leads to shocking repercussions for the whole unit.
Episode 6
Whilst undercover, Church is employed by a brutal mercenary, Cameron Fraser, to assist in the abduction of a young girl at the centre of a bitter custody battle. After a botched abduction attempt, Fraser successfully tails Church putting the security of the Unit at risk. When the girl vanishes, Angie embarks upon a frantic hunt to find the girl before Fraser does.
Episode 7
Following the drug-related death of a young nightclubber, the unit attempts to crack a large-scale Ecstasy racket by targeting its ring-leader. Undercover as a middleman between the dealer and Church, who is posing as an interested buyer, Stone finds a way into the racket through Hannah and Clare, two English backpackers. As Stone gains the dealer's trust, he grows particularly close to Hannah. Stone and Church set up the buy hoping to draw out Mr Big, but a sudden change of plans has devastating ramifications for Stone and Hannah.
Episode 8
Mackenzie goes undercover in the Witness Protection scheme to befriend Carol Jamison, who was nearly killed before giving evidence at a Parliamentary Inquiry into corruption. Carol claims no knowledge of corruption, remaining loyal to her boss, Member of Parliament Richard Taylor. The attempt on her life remains a mystery. With Mac undercover as a "protected witness" and Church, Angie and Stone in support, Mac must get closer to Carol, gain her trust and persuade her to reveal the information which will incriminate her boss and hopefully shed light on her attempted murder. A genuine friendship grows between the two women, a bond Mac will ultimately have to betray to complete the job and save Carol's life.
Episode 9
While taking part in a drug deal at a suburban service station, Church and his dealer inadvertently get caught up in a siege instigated by three young delinquents. Hostages are taken, and while Mackenzie is able to glean information via Church's wiretap, Rocca works from outside the service station as a negotiator, trying to appease the young hoodlums. As the drama inside escalates, reaching a dangerous, life-threatening level, Church must rely on his undercover skills to defuse this volatile situation from within, preventing the bloodshed of innocent bystanders.
Episode 10
The Internal Investigations Unit, led by the tough Detective Senior Sergeant Vic Slater, takes over the Factory and investigates Undercover for corruption. Slater turns up evidence that results in Rocca's suspension it appears Rocca has tampered with a drug sample and money has turned up in his safe unaccounted for. The unit is in shock and Church, sensing a set-up, is determined to find out what's going on, but Mackenzie who is left in command, tells Church to leave things alone an order that only makes him more determined.
Episode 11
Rocca forces Church to drop his long-term informant, Benny, after Angie is put at risk during a drug bust. Benny, who to Church has become more friend than informant, is outraged. Benny sees himself as a quasi-undercover operative who has been unfairly dismissed and offers to help Undercover prevent an armoured car heist. It will be Benny's "last hurrah" so he wants a healthy retirement package. He feeds information to the Unit piece by piece, playing the ultimate power game. Suspecting that Benny may be stringing them along, Rocca puts Mackenzie in undercover at the armored car company to find out whether the robbery could be an inside job.

Episode 12
Church sets up an undercover deal with a gang that goes disastrously wrong when Stone is hit over the head and falls into a coma. Emotions run high within the Unit as Church is forced to remain undercover following information that the bikies are involved in a large-scale counterfeiting. Angie spends time with Stone's father at hospital, she must try to appease a man who knows nothing about his son. Church increases pressure on the Bikies regarding the counterfeit notes, ultimately becoming the Bikies' prisoner. Out on her own, Mac uses her computer expertise to prevent the counterfeiting, but is taken prisoner by the gang.
Episode 13
Stone is nearly shot during a meeting with a dealer. When an informant helps Stone, Mac is concerned about how it will effect Stone's already rattled state of mind. Meanwhile, Angie has established her first informant relationship and is using this to bust a drug dealer. Angie and Stone's contacts lead them to the same place, jeopardising each other's stings. Stone stays undercover and saves the guns deal and succeeds in bringing down the gun dealer. Angie's work reveals that Stone's informant had been using the gun racket to cover her own dealings in drugs.

Episode 14
The unit goes undercover to locate a charismatic prison escapee, the media-agile crim Bobby Kane, who accuses the police of wanting him dead rather than recaptured. Angie is put in as a cameraman working for Trish Lambert, an ambitious television journalist Kane uses to air his views. Rocca begins to suspect that the investigating policeman, Detective Inspector Gil Truman, who has pursued Kane so zealously since the robbery, might have his own agenda that involves killing Kane rather than capturing him.
Episode 15
Stone and Angie infiltrate a radical environmental group, Mother Earth, suspected of stealing explosives for terrorist activities. Church is then put in prison to befriend the group's leader, Aaron Fielder. Fielder is controlling the "movement" from prison and is formulating a terrorist plan. When Church makes another shock discovery, he decides to pursue his own agenda and, contravening orders, he joins Fielder in his pursuits.
Episode 16
When Church joins Fielder and his group of environmental extremists in their terrorist masterplan, he is surprised to encounter Stone, already undercover with the group. Stone wants to report the latest developments back to the Unit and have the group arrested, but Church pulls rank, insisting that any contact would jeopardise the sting. Stone soon realises Church is driven by his own agenda, and attempts to sabotage the operation before Church, and the terrorist situation, get out of control.
Episode 17
Someone is killing prostitutes Angie and and Mackenzie go undercover at a brothel. When an attempt is made on another prostitute's life, Undercover come up with an obscure clue, but without sufficient evidence, the killer cannot be arrested. Angie is forced to confront the killer and, with help from Church, is able to diffuse a potentially fatal situation.

Episode 18
Church becomes involved with the notorious Rossi crime family when he goes undercover to investigate a murder. Church discovers the murder is not what it seems and begins to ingratiate himself with the Rossis. In a meeting that will change his life forever, Church encounters a surprise member of the Rossi family.
Episode 19
Church attempts to infiltrate the Rossi family hierarchy Bruno, the head of the family, his son, Dino, and their menacing right-hand man, Terry Collis. Church takes a liking to Bruno's daughter, Christina, and manages to weaken Collis' position in the family. Collis tries to turn Dino against Church but it soon becomes clear that Dino has already chosen his right-hand man.
Episode 20
With Church recruited as Dino's new right-hand man, Angie goes undercover to investigate one of Dino's contacts and turns up a clue which could link Dino to a recent murder. Church struggles with his feelings towards Christina as he realises he is falling in love. With Dino in custody, the downfall of Rossi crime family seems imminent. But in an unexpected twist, a new leader of the Rossi family comes to light.
Episode 21
Following Peter's abrupt resignation, the Unit grows concerned over his developing relationship with Christina, so MacKenzie orders Angie and Stone to tail his every move. Church is forced to come to terms with the truth about Christina's involvement with Rossi family business but refuses to testify against Dino. Subsequently, the case falls apart and Dino walks free. Church has joined the ranks of the Rossi family and his betrayal of the Unit appears to be complete.
Episode 22
The Unit continues their investigation into the Rossi family but with Church now on the other side. When someone tries to sell Dino details about Church, the Unit works to prevent Church's cover being blown. Inevitably, the truth about Church's undercover identity is revealed, resulting in a deadly race against time for Church to save his relationship and his life.