Three years after the events of Day 1, Jai is revealed to be in rehab. A body is dropped off by a mysterious van at the Mumbai ATU HQ, where it is diagnosed with a deadly virus. The ATU is informed that it can cause a fast epidemic and kill everyone in Mumbai in a month. Jai thinks Veer (his son) still holds him responsible for Trisha's(Jai's wife's and Veer's Mom's) death and speaks to Kiran about this. Shivani Mallik in the ATU thinks Haroon would try to expose this virus in Mumbai through his drug network. With the help of Haroon and Gyan, Jai visits Roshan in Pune Central Jail to plan a prison break.

Jai informs Roshan that Haroon has sent him to break him out of prison before he is hanged to death. Haroon calls Gyan to check the progress on the prison break. Omkar (Maya's father) disposes of the body of the man Haroon killed earlier and warns Maya not to run away, as he is scared of Haroon thinking he might kill him and Maya as well. Naina visits Aditya and Prithvi in Mumbai and urges him to free Divya as she is family. Naina insists that she will handle people like Yadav. Maya calls Jai and informs him about a big consignment coming that night and that he is planning to leave India and she is not interested in leaving without him. Shivani informs the Home Secretary, the Police Commissioner and Prime Minister Aditya Singhania about the weaponized virus and the threat that they received to free Roshan. She also says that they have only 6 hours to work on it. Aditya instructs everyone to move Roshan to a highly secured cell and ask for Jai's whereabouts. This foils Jai's original plan and he asks Gyan to send him the blueprints of Pune Central Jail. In Pune Central Jail, BST delivers the bomb to Muzaffer. Jai detonates the bomb set by Muzaffer and informs Gyan that everything is in control to free Roshan and asks him to update Haroon as well. At the end of the episode, it is revealed that Gyan is a mole in the ATU HQ.

Kiran shows the decorated house to Veer having seperate spaces for her brother and her dad. Aditya and Prithvi conduct a meeting with all pharma companies regarding the health bill which would be presented in Parliament next week. Aditya says that it would reduce the cost of most life-saving medicines. Kush (the drug carrier) pays 2 months' rent in advance to his landlord. His parents ask him about where he got so much money from and find out that he sells drugs. He has a narrow escape when the ATU raids their house and the ATU notices that some cocaine was thrown into the wash basin by Kush's mother to hide it. The ATU suspects that it has made its way to the sewage system and that it needs to be contained as they suspect it has the virus in it. In the meantime, Roshan kills the inspector in his cell. Veer shows the video of Jai and Maya to Kiran to prove his point that Jai is having an affair. Gyan's colleagues in the ATU suspects that he is wrong when he leaves the desk frequently to update Jai and Haroon. Haroon scolds Jai to do his job as he is paying 25 crores to him and not to bother about Roshan's doings. The ATU doesn't find any virus in the cocaine found in the raid. At the end of the episode, Shivani figures out that virus is inside Kush.

Kush is captured by haroons men. Haroon updates maya about the meeting at 8 in the night and also tell her that Jai is helping them to get Roshan out of jail. Jai asks Gyaan to send a fake mail to jail Superintend Joshi. Maya questions Jai about his true intentions, why he is trying to free Roshan. In the episode end, ATU gets to know that Jai was present in the jail during Roshan's cell transfer and they let S.P. Joshi know that Jai is no more working with ATU and Joshi here's this with Jai sitting in front if him.

ATU chief Shivani asks Gyan to send an alert about Jai across all departments. Kush and his girlfriend know about the virus he is carrying. Jai shows Superintendent Joshi his son's picture and asks him to follow his orders to free Roshan. BST sabotages the electricity supply of Pune Central Jail to help Jai. Many cells catch fire creating chaos and the Jail Officials start opening the gates. Superintendent Joshi gives an order to start the Code Red Protocol. Haroon is furious about Jai's plan and asks Gyan for updates. Jai takes advantage of the outbreak and along with Roshan impersonates 2 police officers. Jai is caught up by a group of prisoners and they force him to play a round of Russian Roulette. BST gets killed in this. This episode ends with Jai and Roshan playing the game and one bullet sound is heard while the screen cuts to black.

After many hiccups, Jai is able to reach the control room and takes S.P. Joshi hostage. Kiran finds out the truth about Milli's mom Sara and asks her to seek the help of police when Inder arrives. Kiran runs away with Milli while Inder was stopped by Sara. Kush attempts committing suicide when his girlfriend Mitali falls asleep, but Mitali successfully saves him. Naina Singhania visits Dr. Devyani Bhoumik when she meets Dhruv over coffee and sees everything. Naina tells Devyani to leave Aditya alone to which Devyani replies back by telling her to leave Aditya and her alone. Zara tells Raj about Chang's hideout and he rescues Kush and Mitali. Naina asks Khosla to get each and every piece of information about Devyani. Colonel Sudeep from RAF updates the PMO about Jai's attempt to free Roshan. Aditya questions Shivani about Jai's involvement and orders her to come to the PMO. Shivani hands over charge to Gyan and leaves for the PMO. Meanwhile, Jai and Roshan manage a narrow escape with Superintendent Joshi as hostage. The Home Ministry issues a shoot at sight order against Roshan and Jai. Shivani hears this and requests the PMO to dismiss this order as they have S.P. Joshi with them. The PMO realises that Mallik is trying to defend Jai and labels him as 'traitor' and dismisses her request. In the end of the episode , the police and RAF strengthen their search efforts to capture Roshan and Jai; Gyan calls Haroon and tells him that Kush has been rescued and that Roshan and Jai are out of the jail.

Jai's car decoy works and he manages to reach the extraction zone with Roshan, while Salim misleads the police in an ambulance. Gyan holds Zara captive inside the server room, as she sees the glimpse of his activities with Jai and Roshan. Meanwhile, Inder makes Kiran struggle by filing a police complaint against her. Being suspicious about Jai, will Roshan be able to trust Jai?

The PMO knows that someone is helping Jai from inside and assigns Siddharth Sehgal (Mallik's ex-husband) from the Intelligence Bureau as the ATU chief. Siddharth reaches the ATU HQ with Veer and takes charge. He instructs all the agents to tap into the surveillance footage of the highway, tap into Jai's cell phone and asks Gyan to check who sent the fake clearance to ambulance. Salim is caught and sent to Panvel police station. Roshan asks Haroon to not trust Jai and Haroon tells him that he is the only one who can take them out of the country and then Roshan is free to do anything with Jai. Maya gets to know this. Sehgal updates the PM about recent updates and Mallik insists on going back to the ATU HQ and Aditya agrees with her. On Sehgal's order, Veer tries calling Kiran to come to the ATU HQ for debrief, but she doesn't pick up. Aditya visits Naina when she tells him about her meeting with Devyani and her ex-boyfriend. Mihir has to do Zara's work and asks Gyan about her whereabouts. Kush's condition is getting worse and his parents visit him. Veer is on his way to meet Kiran where she is, in the hospital which is locked down for an hour. Naina surprises Aditya when he is on a call with Devyani. Mihir still sees network issues and visits the server room, but is unable to enter in it as access code were changed by Gyan. Gyan is trying to escape the ATU HQ when Mihir resets the password and enters the server room. Zara tells Mihir about Gyan and Sehgal orders the ATU to be locked down to catch Gyan and take him into custody. Vedant gains his consciousness and hears all the updates and insists on going to the ATU HQ as soon as possible. At the end of the episode, Roshan tries to cut Jai's finger with a knife and they get into a fight but Jai gains the upper and asks for a rope to tie Roshan.

While interrogating Gyan Haroon gives him a call, but ATU fails to trace it back. Khosla updates Naina about Dr. Bhoumick's background details, tells her that she was a drug addict. Vedant reaches ATU and asks Mallik to be there soon. Finally Haroon meets Roshan who was having his hands tied. Mallik asks Siddharth to let her and Vedant talk to Gyan. Veer calls Kiran, but that call is answered by her neighbor who is badly injured. Siddharth is losing his patience as he is pressured by higher authorities and starts interrogating him. Gyan cell received a signal which indicated that Jai, Haroon and Roshan are together. Mallik then tells Siddharth that this whole thing was an undercover operation and only she, Gyan and Vedant knew this and keep insisting that she wants to talk to PM. Mallik along with everyone involved in this operation gets in a conference with PM and updates them about the whole operation. She tells everyone that Jai did all this to gain confidence of Haroon and stop the virus attack. She also updates the PMO that the virus delivery is scheduled at 8:30 p.m. Aditya is furious that they have freed a man who is responsible for killing thousands of people. Siddharth backs Mallik and asks PM to support Jai so that they can get the virus. Mallik playa a video where Jai updates everyone about the reasons of all this being kept a secret. Aditya is left with no other option than to support this mission and let everyone know that all would go through an enquiry. Prithvi tells Aditya that he thinks ATU did the right thing by not telling others as they didn't want to put him in jeopardy. Khosla sends an email to hospital officials with some information about Dr. Devyani. Kiran tries to rescue the kid but her attempt fails as they are captured by kids father. In the end, Haroon shows a video about the deadly virus to Roshan and tells him that they got a 500 crore contract to release this in 6 big cities in India and virus delivery is at 8:30 pm.

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Jai updates ATU that deal us going to happen in south east direction in 15 mins, but Maya listens his conversation. Jai explains her his reasons and asks her to go to ATU backup team placed at 2 km. Siddharth calls Kamat to stay alert and wait for Jai's signal. Meanwhile, Aditya denies to remove Prithvi from his staff. Naina threatens Mane Shinde that she will reveal secrets from his past if he keep on pilling Aditya' strings. PMO is having a meeting with all the pharma heads where ATU doctor shares the video came from terrorists and requests them to come up with an antidote. Kamat reached at the exchange location where he sees everyone and shares photos with ATU. Jai and Roshan asks for a retest for all 6 tubes containing virus. Jai gives go ahead to Kamat. Drug dealer asks Roshan to kill Jai, but Jai and Haroon gets into a fight where Haroon and Roshan gets killed. Jai asks ATU to follow the dealer. Kamat reached the site and updates ATU that both the brothers are dead and virus is secure, but Roshan killed him. Haroon asks him to free him from all this pain. ATu backup team reaches the location and finds that everyone is killed using a grenade and Haroon is dead along with one more dead body which is completely burned. Roshan's decoy works as he leaves his leather jacket and escape with a virus tube. ATU is trying to crack the safe containing the virus. Jai asks ATU to send backup and continue chasing the drug dealer. Maya leaves the base with her father to meet the backup team. Backup team who were chasing the drug dealer catches his car and they were attacked by someone hidden in the bushes. At the episode of the episode, Jai reaches in time and catches the drug dealer and fires a shot.