BAAGHI 3 is the story of a man against a terrorist organization. Ronnie (Tiger Shroff) is the younger brother of Vikram (Riteish Deshmukh). Their father was a cop, Charan Chaturvedi (Jackie Shroff), who had died when both were young. Charan knew that Ronnie is braver out of the two and hence he made Ronnie promise that he'll take care of Vikram. When they grow up, Vikram joins the police force at Lohamandi Police Station, Agra.
On his first day of joining, a goon named Bajwa sets a person on fire inside Lohamandi Police Station premises. Bajwa's senior IPL (Jaideep Ahlawat) comes to the rescue and the cops don't press any charges. This is because IPL is a feared criminal by locals as well as the police. IPL's main business is into kidnapping the entire families but he never asks for ransom. This has always baffled the cops. What the police doesn't know is that IPL works for Abu Jalal Gaza, the leader of Jaish-E-Lashkar, the biggest terrorist organisation of the world. They operate out of Syria and have almost taken over the country. Back in Agra, the Lohamandi Police Station gets a kidnapping complaint. Knowing that it's committed by IPL, they fear taking action.
Hence, they decide to send Vikram as scapegoat. Vikram is terrified and he asks Ronnie for help. Ronnie accompanies Vikram at IPL's factory, where the kidnapped people are held. Ronnie bashes up IPL's goons by shutting off the lights. Everyone assumes that Vikram is the one responsible for beating them and for rescuing the hostages. He becomes an overnight hero.
Vikram meanwhile gets married to Ruchi (Ankita Lokhande). Her sister is Siya (Shraddha Kapoor) and she starts dating Ronnie. Life is going good until the Ministry Of External Affairs sends Vikram to Syria. He's given the responsibility of getting IPL arrested and facilitate his extradition process. It seems like a fairly easy task. Vikram reaches there and this is when he gets abducted by Abu's men. With no other option, Ronnie now decides to go to Syria to rescue Ronnie. What happens next forms the rest of the film.