Season 2 picks up six months after the human trafficking case. Azrul has been sentenced while Yusuf faces scrutiny following Jamal's death. Tensions rise with Natasha stepping in as the new leader. Meanwhile Yusuf gain a new ally in lawyer Benjamin. With every case, they uncover a dark figure orchestrating the youth crimes.
6 months after capturing Azrul, Yusuf still struggles with the loss of Jamal as the team moves on with a new leader, Natasha, and a new team member, Hasif. Meanwhile, Maria has started working at the law firm, striking a friendship with Benjamin K. The team is called in when a body of a teenage boy is found with the bully as the main suspect.
The case gets more intricate as it unfolds when the principal becomes a prime suspect. Maria continues to visit Azrul in secret as she tries to find a lawyer to help with his case. The divide between the team is apparent as Yusuf clashes with Natasha during their investigation. A discovery leads the team to the killer as they uncover another crime behind the motive.
The team is called in when a series of vandalism has been happening in the same estate. They soon realise there's a message behind the vandals as they narrow down the suspect list to the estate's potential community leader, Joshua Ng. Maria seeks Ben's help with Azrul's case as he weighs his options. She then receives a text from an anonymous person, aware of what she's been up to.
The group of vandals come to a head when they were almost caught by the S.P.Y team. Alyssa catches Maria in a lie as she starts to tail her. With 2 of the vandals caught, Alyssa follows the lead on a new suspect much to Yusuf's chagrin. Although initially hesitant, Azrul finally agrees to let Ben help him with his case as Alyssa confronts Maria.
S.P.Y investigates a case of a missing girl, Calla, a foreign student with no record of leaving the country. Meanwhile Ben continues to be active at the youth home as he suspects something amiss. Tension arises when the case hits close to home with Hasif's brother arrested. The team finally locates Calla, but nothing is what it seems. Azrul receives an unexpected visitor.
The team continues to work on the fraud syndicate case. Hasif sets out on his own investigation after being benched, but he needs Alyssa's help. Ben starts working closely with Azrul on his case as the two build a rapport. He is also trying to find out what's going on at the youth home. Natasha and Yusuf finally put their differences aside. Yusuf is arrested for Jamal's murder
A girl suffers from acid burn injuries as S.P.Y is called into action. Hasif and his brother, Nizam, try to mend their relationship. Yusuf is being questioned as Maria realises her grave mistake in trusting Azrul. Ben refuses to let Maria get in his head as he continues to defend Azrul. The team looks into a suspect for the acid case, Farhan who has ties to Ben's youth home.
Yusuf is finally released from custody as he learns of Azrul's fate. The team starts investigating Access Youth Home after claims of abuse went viral. Maria struggles to move past everything that had happened. Yusuf enlists Ben's help with the youth home investigation while Frances gets to the bottom of things on her own. An elaborate plan helps the team catch the real perpetrator as the new big bad is revealed.
A series of acts of arson set the SPY team off into investigation mode. Rebel youths, a masked figure, a veteran firefighter, and an aged hoarder make up the suspects in the investigations that ensue. Meanwhile Ben provides advice and delicate support to one of his mentees who is behaving dubiously. Hasif struggles to juggle work with handling his teenage brother Nizam who is drifting away from him.
Natasha, Yusuf, Alyssa and Hasif investigate two deaths involving a middle-aged businessman and a young undergraduate. The team then discovers that a group named Anak Merah are involved. Relationship between Hasif & his brother Nizam is on the mend when the team discovers that Nizam is linked to Anak Merah's operations.
Hasif is heartbroken when he learns that Nizam is involved in the case he is investigating. Meanwhile, the team realise that the death of the middle-aged business man and the young undergraduate students may be connected to the same group - Anak Merah.
The team investigates a case where 13 Secondary Schools simultaneously received bomb threats and realise the threats may have originated from someone within the school itself! Meanwhile, Yusuf uncovers something unusual at Ben's therapy sessions.
The S.P.Y. team was shaken when a bomb exploded within their HQ and threatened to take the life of one of their key personnel. Their investigations on the explosion uncovers a sinister plan by a radical youth group who calls themselves P.L.E.C.O.