Immediately after the events of The Raid, Rama, Bowo, and Wahyu are sitting in an undisclosed location with Bunawar and two of his men. He tells one of them to take Bowo to the hospital. After he leaves, Bunawar orders his other man to kill Wahyu. Rama becomes angry but Bunawar tells him that he was a dead man anyway. He then tells Rama that his life and his family are in danger after what transpired in Tama's apartment building. He asks Rama to be part of his undercover team in order to take out all the corruption in the police force, along with Bangun, Goto, and Reza, the top criminal heads. Rama refuses, explaining to Bunawar that while their goals are the same, their methods are not.
In the aftermath of the apartment block raid, Bunawar presents his superiors with all the cops' files, except Rama's. He claims there were no survivors. Watching from behind a mirror, Reza tells another man that he will 'keep looking', presumably for any loose ends that may threaten to expose them.
Later, we see Rama and his father mourning the death of Andi. This convinces Rama to take the job from Bunawar. His family is relocated somewhere safer. His first order from Bunawar is to get close to Uco, Bangun's son, who is in prison. Bunawar tells Rama to beat up the son of a politician who Uco is enemies with in order to gain his trust and would lead to his arrest.
Rama is in prison, sitting in a toilet stall when he is suddenly attacked by Uco's men. He fights them all before being overpowered. He later sits in his cell, bruised and beaten-up, punching the wall several times as practice. At lunch, Uco goes up to Rama, who calls himself 'Yuda', and tries to convince him to join his side since he defeated fifteen of his men. Rama declines his offer. During visiting hours, Uco meets with one of his father's underlings, Eka, who wants him to have extra protection since his life is in constant danger. He tells Eka that he is curious about Rama/Yuda, but is told that he isn't of interest. Meanwhile, Rama meets with one of Bunawar's men who tells him that he has to stay in prison for three years, not months like he was promised, due to the politician's anger.
In the prison courtyard, the prisoners sit away from the rain. Rama starts to notice some of the prisoners on the other side signalling to each other and passing around a shank. Three of them approach Uco who is sitting a few seats away. Before they could strike, Rama uses a broom handle to fend them off and saves Uco's life. This insinuates a riot out in the courtyard, where the prisoners and guards begin to fight each other in the mud. Some prisoners are shot dead as they try to climb the prison fence. Uco is attacked several times and when he is almost unconscious on the ground, an attacker goes over to finish him off. However, Rama steps in and once again, saves Uco. He is later knocked out by a guard, but not before catching Uco's attention.
Two years later: Rama is released from prison. He notices a wire on his jacket and immediately tears it out. Outside, he is met by Uco, who had him released a year early. He takes him to his father, who wants to thank Rama personally. In Bangun's place, a meeting is going on between Bangun and Goto where they discuss the uprising of Bejo. After Goto and his man, Keiichi, leaves, Uco brings Rama before his father. He tells Rama to strip all of his clothes off to see if he can be trusted. They check his clothes and find them to be clean. He is given new ones along with a penthouse. There, Eka, one of Bangun's men, gives Rama a cryptic message before leaving him be.
After he's alone, Rama blasts music really loudly and calls Bunawar using a SIM card he'd hidden in his mouth. He argues with his boss that he almost got him killed for having that wire on him and that he will do things his way from then on. After that conversation, Rama calls his wife. He asks her if he can listen to his son for a while.
The next day, Uco, Eka, Rama, and two other henchmen go to an underground porn industry where they demand payment from them. The leader, Topan, refuses to pay the extra 5000 after he is caught importing drugs. One of his men reaches under the table for a concealed shotgun. Rama notices and immediately stops him. A firefight ensues, leaving all of Topan's men killed along with two of Uco's. Topan escapes and Rama gives chase. He catches him in a room where he mercilessly beats Topan but stops himself from dealing a killing blow.
Eka compliments Rama's skill to Bangun. Uco then asks his father when he can move on to bigger things than simply collecting debts. His father says he isn't ready to move on yet, which angers Uco. Later, at a club, Uco begins to abuse one of the working girls and threatens her when she begins to insult him. When the manager steps in, Rama tells the girls to leave. When the two men are alone, Rama tries to reassure Uco that his father will come around. Uco's phone rings and he steps outside to speak to the mystery caller. Rama takes the opportunity to place a wire in Uco's wallet.
Meanwhile, Bangun meets with Prakoso, one of his most trusted hitmen who is also a homeless person. He gives him an envelope containing a new target. Prakoso is later sitting by a curb with his machete by his side, waiting for his target to appear. When he sees him and his guards with him, he quickly fends them all off and gives chase to his target. When they are both at a dead end, Prakoso impales his target with his machete.
Rama meets Bangun the next day where he warns him on the matter of trust and ambitions. It is revealed that he killed Topan and his men dumps his body in a lake. Bangun recognises that Rama is best positioned to keep an eye on his son and asks to be kept informed if anything important comes up involving Uco.
Later, the person who called Uco is revealed to be Bejo who wants to cause a war between Bangun and Goto, claiming both territories in the aftermath. Bejo seems to be a practical man and appears unconcerned with history and tradition. As a gesture of goodwill and a show of commitment, he brings forth five former prisoners who attacked Uco and lets him to execute them all. As Uco goes to slit each of their throats, they discuss how they will be able to cause a rift between the two families. Before killing the last one, Uco notices a distinct tattoo on the man's wrist. Bejo says that they will need to kill a trusted man in Bangun's family and not just a foot soldier. Outside, Rama listens in on their entire conversation and then watches them both leave.
At a restaurant, we see Prakoso meeting his ex-wife, who berates him for being an assassin. He asks if he can see his son, in which his ex-wife refuses. He later gets a message from Uco and leaves early. They meet up at a dance club where Prakoso tells Uco to be patient with his father and that he has the same fiery ambition within him. Uco goes to the bathroom. Prakoso takes out a locket with a picture of his son in it and stares at it for a while. He soon realizes the entire club becomes empty. The doors swing open and numerous men come in. Prakoso starts to fight these men. The fight leads to the alleyway, where Prakoso gets sliced numerous times but not before finishing off the last man. He sees Bejo's Assassin on the other side of the street and realizes he is finished. Taking out the locket, Prakoso faces the Assassin, who leans in to look into his victim's eyes before quickly finishing him off with his two knives, all the while Uco is watching.
At Bangun's headquarters, Uco pretends that Prakoso was killed by the Japanese, Goto's men. He demands retribution from his father but Bangun shoots it down, stating that he does not want to ruin the peace between the families. Rama comes in and is told to go calm Uco down. He tries, but fails. Uco calls Bejo and tells him to continue with the plan, regardless of Bangun's approval. Bejo then orders his three assassins, the nameless one that killed Prakoso, Baseball Bat Man, and Hammer Girl, to hunt down specific targets from Goto's family. They all find and kill them along with their guards.
We see Rama get into a taxi where suddenly he is surrounded and attacked. He barely escapes and goes into a restaurant where he defeats his pursuers. After finishing the last one off by pressing his face down on a grill, Rama sees that they are all police.
At a meeting between Bangun and Goto, the two are ordered to repair their truce or forcibly disband their families. Bangun agrees and takes full responsibility for everything, much to Uco's anger. At Rama's penthouse, he treats his wounds and angrily calls Bunawar about his pursuers. He later gets a call from Eka who tells him to get to Bangun's immediately. Father and son are having a falling out where Bangun beats Uco up for provoking the Japanese during the meeting. He then finds out that his son is directly involved with the growing feud between him and Goto.
Uco's betrayal is compounded when Bejo and his men arrive to confront Bangun. Uco takes his gun out and points it at his father. Looking away, he shoots Bangun in the head, point blank. Eka calls Uco a traitor and takes his gun out, which prompts Uco to shoot him in the leg. Bejo takes the gun from Uco and prepares to finish Eka off when Rama interrupts. He quickly disarms Bejo and fights with the Assassin, telling Eka to run. The Assassin overpowers Rama and defeats him swiftly then Bejo orders his men to take Rama away.
Eka watches as Rama is dragged into a car. A convoy of Bejo's men then drive him away. On the way, he receives a call from Eka, who is in pursuit. He collides his car with the one Rama is in, inciting a car chase. Rama fights the men holding him captive while Eka takes out the accompanying vehicles. After dispatching his captors, Rama escapes through the back, jumping on to Eka's car. The two make it out of the chase alive.
During a meeting between Goto and Keiichi, they learn that Bangun was killed by Uco, who allied himself with Bejo, and Reza is off to a meeting with them. Concerned with this new alliance, Goto decides to 'start over' and declares war on Bejo and Reza. At a ruined site, Eka pulls over and reveals to Rama that he knows he is an undercover cop and that he was one too. Bleeding to death, Eka tells Rama that only by taking out everyone at once can the conflict be ended. He leaves the car and dies peacefully while Rama drives away.
He calls Bunawar and argues about Eka, wondering why his presence was kept a secret. Bunawar reveals that Eka fed him bad intel, which led to ten cops dying, and is disgraced. Rama asks his boss if his family is safe and will remain that way, in which Bunawar assures they are and will be. Rama then hangs up on him. He is outside Bejo's restaurant where he drives through one of the garages and alerts his men. While he fights them, Uco is in the bathroom upstairs, bruised and beaten. As he is about to tip the towel boy, he notices the wire. He goes back to Reza and Bejo sitting at the table and remains silent throughout. One of the henchmen warns Bejo that Rama escaped custody and is now in the building. He orders everyone to kill him, sending The Assassin, Baseball Bat Man, and Hammer Girl. When Bejo accidentally drops his cane, Uco looks down and notices the same tattoo that was on one of the former prisoners he executed.
After finishing everyone off in the warehouse, Rama moves up to face Baseball Bat Man and Hammer Girl. They fight, leaving Rama injured and both assassins killed. He moves on to the kitchen where, after the entire staff leaves, he faces the Assassin. The pair engage in a lengthy and very brutal fight, with Rama having the upper hand until The Assassin takes out his two curved knives. Rama disarms and takes one of the knives, where the two begin to slash each other. Rama finishes the Assassin off by cutting his arms and slicing his throat.
Bloodied and worn out, Rama pushes himself through, interrupting Bejo, Uco, and Reza. He fends off two guards while Bejo runs over to the bar to grab a shotgun. He throws it to Reza but Uco takes it instead, shooting and killing Reza. Bejo starts to shoot at Rama, who runs and takes cover, but is wounded by him. Uco then points the gun at Bejo and shoots him in the leg and then the shoulder. Standing over him, Uco drops the wire by his head, points the shotgun at Bejo, and blasts his head off. He then turns his attention to Rama taking cover behind the couch. He shoots relentlessly but has to reload. Rama takes the opportunity, jumps over and stabs Uco.
At the end, Bunawar races over to Bejo's restaurant while Rama walks back down to the warehouse. There he sees Keiichi and his men waiting at the entrance. An unheard conversation goes on between them, ending with Rama simply saying, "No...I'm done."