The story starts with a scene from 1995, in Purilia, West Bengal. There are a lot of locals working on a farm and getting pictures clicked by a journalist when suddenly a military plane passes by and drops illegal ammunition items in the field. An entire controversy follows and the case is called Purilia arms drop case. There is a sudden switch to the present day situation where Shruti (Katrina Kaif) is launching her set of comics- Jagga Jasoos. Along the lines of a recital Jagga’s character is introduced swiftly. Jagga (Ranbir Kapoor) is an orphan kid who is left at a hospital which gradually becomes his home. He is a shy kid who doesn’t talk much because he stammers. One day he comes across an injured man on the ground near his hospital, who is the same journalist from the Purilia arms drop case. Jagga rushes him to the hospital. The journalist starts recovering slowly and gradually, and Jagga would come to see him in his ward every day religiously.
The journalist kept on asking Jagga his name but Jagga wouldn’t answer him. Finally someone tells the journalist that Jagga doesn’t talk as he stammers. The journalist goes to Jagga, and gives him and idea of singing whatever he wants to talk about as one does not stammer when he/ she sings. Jagga does that and is surprised with the result. Jagga asks the guy his name and he tells Jagga to call him Tooti-Phooti. The two start growing really fond of each other and finally, Tooti-Phooti alias Badal Bagchi (Saswata Chatterjee) adopts Jagga. All is going really well for the both of them until a man with a couple of subordinates randomly comes to catch Bagchi and they decide to escape from their house then and there. The man leaves a letter for Bagchi, which after reading, Bagchi decides to enrol Jagga in a boarding and leave for whatever work is given to him.
Jagga is a grown up boy now, who has grown up with all his other friends in a boarding in Ukhrool. There is again a switch over to present day, where Shruti tells all the kids at the book launch about the first book of the series, Jagga Jasoos and the case of the clock tower. We are again taken back to the school. Its shown that Jagga has taken a fondness towards being a detective and deducing things in his own singing manner. The first case is about the death of the English teacher Ms. Mala, that Jagga solves by relating and joining all the little clues and hints. He discovers that it was not a suicide but a murder which was plotted by the PT teacher and his wife, and he is successful in bringing out the truth as well. Jagga’s birthday comes the following day and they are all enjoying and partying and as usual Jagga is waiting for his birthday tape to arrive. Bagchi sends a tape a year to Jagga, telling him all that a father wants his son to know and much more. It’s the happiest day of the year for Jagga. Meanwhile its shown that Bagchi has started working for Sinha (Saurabh Shukla) and he is required to click pictures and bring out leads for a topic the audience is unaware about as of now.
We are again taken to the book launch day, where Shruti then talks about the second book in the series which she proclaims is her favourite case. Switch to the case, Shruti Sengupta comes to Ukhrool, she is a journalist from London who comes there to find about the illegal ammunition racket going on. Jagga is instantly attracted to her because she is as goofy and comical as his father, Tooti-Phooti.
Jagga follows Shruti to her lodging abode, where he comes across a suspicious man, who he follows. The man goes to a small house where there is an injured man and a doctor, the injured man has the doctor on gun point. Just as Jagga is calling the police inspector, there is a gunshot, the injured man is dead. Later in the evening its shown the same man who Jagga bumped into, calls Shruti up and asks to meet him in a fair. The two meet and Jagga follows, but this man is killed as well and Shruti is the suspect. Jagga wants to know the truth so he goes to Shruti’s room and demans the truth. Shruti tells Jagga that boh the guys who died were ex-militants who were giving her inside news related to the illegal ammunition racket.
Suddenly, the police comes to the lodge as they are on a lookout for Shruti, but Jagga makes Shruti run away with him. Suddenly we are shown that Shruti had a fiancé who was a fellow journalist with her, but the head of this racket killed him right in front of her eyes. Shruti wants to expose this racket at any cost, so Jagga starts reading all about the illegal supply of ammunitions and finds out a tunnel which was the headquarter for this. The duo go there and bust the racket somehow. Shruti is really happy and goes back to her house assuring Jagga that she will be there for him whenever he needs her.
One more year passes by and its Jagga’s birthday again but this time there is no tape. On the parallel side its shown that Sinha tells Bagchi that he doesn’t want him to work for him anymore and while Bagchi is driving he meets with an accident as he crashes into a tree. He has an important tape on him that Sinha’s men take away. Sinha heads a group of people who blackmail powerful and influential people. At one such incident Sinha is showcasing one of his tapes as an evidence to a politician when he realises that his real tape has been exchanged with one of Bagchi’s wishing birthday to his son Jagga. Meanwhile, Jagga waits everyday for the postman to come but there is no luck. One day the news comes out that Badal Bagchi is dead and a prayer meeting is organised for him in Kolkata so Jagga heads for Kolkata. There Jagga meets sinha who tells him that he is the same man who sent Bagchi a letter years ago which is why he left. He told him he worked for intelligence and demands his original tape back. Jagga says he doesn’t have a tape and his father cannot be dead. He escaped from Sinha and lands up at Shruti’s house. Shruti tells Jagga all about bad luck Bagchi. How he was a good journalist who wanted to bust the illegal ammunition system after the Purilia Arms Drop case in India and all over the world but who was tangled in the politics in such a way that a case of a murder of his colleague Samar was charged on him. Bagchi had to run away and escape and while escaping he fell of the train and injures himself, and that is exactly when Jagga had found him for the first time. Jagga forces Shruti to come to Mombaca with him from where Jagga got a telepost of his father from.
The two of them leave on a look out for Bagchi in a certain hotel, which were around 98 in Mombaca. They earn money there by dancing and checking off hotels everyday. Sinha follows the two in the search of his tape, although even after getting the information that the tape is with sinha’s men, he needs to kill Jagga and Shruti as the politician asks him to. Slowly and gradually Shruti and Jagga have a grown fondness towards each other but Shruti starts feeling as if she is cheating her ex fiancé and wants to go back to India. Jagga somehow makes her stay and atlast they get a lead to a hotel where Jagga finds his photos and all his memories attached on a wall. Its Bagchi’s room. Suddenly Sinha comes and Jagga and Shruti somehow escape once again leaving Sinha and his men behind. Jagga and Shruti are running away in a car just when their car hits the same tree that Bagchi’s car did. There through the tribals they get to know that Bagchi spends quite a lot of his time there. They find his diary in which they get to know about Bashir Alexander who runs the biggest underground arms fair and who was responsible for the Purilia Arms Drop case as well.
With this information now, Jagga and Shruti set out to find a circus train that was mentioned in the diary that his father was on too supposedly. They finally find the train and enter it and Alexander is inside it. Alexander is a prodigy and has two head but one body. He believes in the concept of ‘divide to sell arms and mass attacks’. Jagga wants to unveil what his father wanted to do now. After two-three attempts Jagga and Shruti enter the train with the ammunitions. Bagchi is one of the militants on the train who Shruti pushes off the train. Jagga being Jagga, replaces guns with food and cakes its shown hence making every place a happy place. While escaping from the train and Alexander’s men, Jagga gets shot, and while shruti looks over to him as she is driving, their car hits Bagchi. Finally after so many years, Jagga and Bagchi meet, and all is good. The three of hem return to India together and he movie again shifts to the present day book launch where one moment all of them are having fun and the next moment, Jagga and Bagchi are kidnapped by Alexander (Nawazuddin) who laughs and on that note the film comes to an end.