Season 3 introduces us to Ed’s younger brother Roy (played by Colin Cunningham) who ignored Ed’s order not to approach the situation, and got his partner killed. A planned raid on an escaped convict sees the man take a teenage boy and a baby hostage at a drive-in motel. Team One raids the room and ends the stand-off, but the teenager inexplicably vanishes. Discovering a hidden trapdoor leading to a sewer and a cache of information that suggests the teenager is a serial killer, Ed leads Sam and Wordy in an effort to stop the boy before he kills someone. However, Parker and Jules discover more information about the boy that suggests he is not a psychopath, but has Asperger syndrome. The second episode is about a woman (Kelly Rowan) who has recently been released from prison and is looking to reclaim her children, who were put into foster care when she was convicted. The girls were legally adopted while she was in prison, however, and she has no legal claim to being their mother. When one of the girls has an allergic reaction, the woman takes hostages in a drug store, demanding that they treat her daughter and that the SRU allow her to leave with her daughters.
Team One is tipped off to a white supremacist group who is planning a spate of bombings against immigrants across the city. The team is able to apprehend most of the members, but three bombers escape and the SRU must find them before their bombs are detonated. One is caught before he can plant his bomb, but his capture alerts his friend, who announces his intention to detonate his bomb in a busy office building. While Sam and Jules try to talk him down, Ed and Wordy chase the group’s leader, who has planted the third and final bomb with the girlfriend of the man who alerted the police. Sam and Jules convince the bomber to give up moments before his bomb detonates, while Ed disarms the third bomb. The leader is taken into custody, but the young men reject his teachings. The SRU responds to an abduction of a high school student, Carlton, but he flees once he has been rescued. He is spotted on the roof of his school the next day, threatening to jump. Parker approaches him, and the SRU learns of a disturbing culture of silence and abuse in the boy’s basketball team. Distraught that the kidnapping has left his friend suicidal, a second basketball player takes the coach hostage as revenge. After talking Carlton out off jumping, the SRU enlists his help to stop his friend. When Team One responds to a “shots fired” call, they discover Ed’s brother, Roy, is deeply involved with an arms dealer. Suspended from duty and suspected of stealing $100,000 from an evidence locker, Roy has infiltrated the arms dealer’s operations as a buyer to prove he is a good officer, and intends to get revenge against the man who sold the gun that killed his partner in “Unconditional Love.” Roy leads Ed and the SRU to the heart of dealer’s operations, but is forced to break his cover to save Jules. The arms dealer shoots Roy before being shot in turn by Sam. Roy survives, as he was wearing a bullet-proof vest. Ed admonishes his brother for being stupid, but also shows him respect for his initiative.
Alexis, a grade-school girl who has built a relationship with a 911 operator over the course of a series of false alarms, appears to be threatened with a real kidnapping that sees her mother shot. When more shots are fired in front of the assembled police and the SRU, Team One learns that Alexis and her family are federally protected witnesses, after she witnessed the murder of her friend by three corrupt police officers, who are now in pursuit. With her mother in the hospital and her father taking one of the corrupt officers hostage, Alexis believes she is left alone in the world. Longing for friends of her own and wanting to finally stop running, she is confronted by one of the officers in a playground before he is shot by Greg Parker. Meanwhile, Greg’s son, Dean, comes to the station. Team One becomes the subject of an investigation into its handling of a horrific killing spree at business party held in a city museum. Facing criticism for taking 37 minutes to bring the situation under control (when similar situations had been contained within 15 minutes), the team members recount their actions. Initially suspecting it was a random killing, evidence emerges that the killings are targeted. The perpetrator is a woman distraught at her husband’s death from an allergic reaction to the binding agent in a drug made by the business hosting the party. When her attempt to force the company to change the drug with a lawsuit fails, she decides to take revenge, killing everyone involved in the case. Meanwhile, Ed discovers that the investigating agent is on a witch hunt as she blames Parker for her partner’s death when he joined the SRU.
After his wife’s testimony on his behalf at his murder trial of their daughter doesn’t go as planned, Frank McCormick (Jonathan Scarfe) finds himself in a prisoner transport van with a fellow prisoner who has an escape plan. Team One initially focuses on the prosecuting attorney as Frank’s likely target for revenge. In a desperate attempt to restore his wife’s (Cara Pifko) trust in him, Frank uses his escape to try and prove the evidence presented at his trial is faulty. After capturing the other prisoner and his accomplice, Team One changes its focus to Frank’s wife as the most likely target, which in turn leads to Frank to take the coroner (Barbara Eve Harris) who performed the autopsy on his daughter hostage. It turns out that his daughter died from a rare disease and not was not shaken to death. As the standoff ends, Ed gets word that his wife is on the way to the hospital due to complications from her pregnancy. What looks like a man anxious to withdraw a large sum of money from his own account turns into a bank robbery. Team One discovers that the man, whose identity was stolen by the bank robber, has been kidnapped, and a ransom of $40,000 is demanded before a bone marrow donation will be done to save Chris, a child with leukemia. Jules goes to the hospital where she finds Ava, the Chris’ mother. She reveals who is the real Chris’ biological father. On Jules’ day off, a man with a handgun holds patrons hostage in a restaurant. The suspect is convinced that there is a terrorist bomb about to go off, and demands the presence of the restaurant owner (who is of Middle Eastern descent) who is accused of being the lead terrorist. The SRU interviews the owner, who admits donating to a charity that was later discovered to be a front for terrorism money laundering, however the federal investigation concluded that the owner was not connected to any terrorists. The SRU also finds that the suspect is schizophrenic, which, combined with recent terrorism news coverage, heightens his suspicious.
When a police car transporting prisoners crashes with a bus, the prisoners escape to the bus with the unconscious officer’s gun. When the police officer responding to the crash is shot, the SRU is called to the scene. When the driver of the car involved in the crash is identified as Sgt. MacCoy from 52 division, Spike is desperate to rescue his mentor. With the bus on fire, the prisoners and Sgt. MacCoy flee. Until a report of a police officer carjacking a woman is received, Spike believes Sgt. MacCoy is a hostage. When it is revealed that he pulled rank to get the prisoner transfer and that he insisted upon doing it without a partner, Spike has a hard time accepting that his former mentor and training officer is involved with corruption, drug dealers, and an attempted gang execution because he was so devoted to taking care of his recently deceased wife and troubled daughter. Jackie (Rachel Blanchard) was caught skimming credit card data and is now working as a snitch on her boyfriend Alexander Carson’s (Tim Rozon) operation cloning, high-limit credit cards of big spenders all over the city. When Jackie reports that the in-person meeting between her boyfriend and Mark Griffin, a big player in data theft who is looking to buy the operation, is going to happen that night at Carson’s club, Detective Merry Danner (Natalie Brown) from the financial crimes division works with Team One to shut them down. Carson’s best friend, Tom (Richard Chevolleau), inadvertently ruins Team One’s plan to contain the bust when he unlocks the interior door to the room where the deal is going down. In the confusion, Carson and Jackie escape, forcing Tom to come with them.
While waiting for a delivery of money from his off-site office, Carson questions who told the police about the meeting. When Tom accuses Jackie of being the snitch, a fight breaks out and Carson shoots Tom. Team One catches up with Carson and Jackie at the airport as they were about to escape on a plane that had already been chartered as the return flight for Mr Griffin. All the while, Ed is struggling with an ultimatum from his wife. In an emotional season finale (but part one of twoparter) Members of Team One try to figure out who has it in for them when a military psychologist (Victor Garber) with the reputation of being a ‘team breaker’ is brought in to run their routine psych evaluations. Meanwhile, Eds life is on the line after a case of bad timing results in being shot more than half a dozen times away from the team.