Inayat Khan is the Senior Superintendent of Police responsible for the security of Srinagar, Kashmir. One day, his young son Irfaan met an accident and is taken to a hospital, but due to a fatwa instigated by the leader of a terrorist group forbidding doctors to treat policemen and their families, the doctors refuse to treat Irfaan. Irfaan succumbs to his injuries. As revenge, Inayat Khan and his men manage to attack and kill all the terrorists hiding in the village of Dalgate.

A family caught in the crossfire is being killed by accident. A young boy named Altaaf is the only family member who survives the shooting as he is severely traumatized by his parents and sister's deaths and haunted by the memory of the masked policeman (who is Khan himself) before falling unconscious. Khan's wife Neelima, feeling sorry for Altaaf, attempts to persuade Khan to adopt Altaaf. Despite fearing that Altaaf may one day discover the truth and get revenge for it, Khan reluctantly agrees as he is wracked with remorse for killing Altaaf's family.

Just when Altaaf seemed to have settled down in his new home and accepted Khan and Neelima as his new parents, he finds Khan's mask and realizes that Khan was one of the policemen who killed his family. After an unsuccessful attempt on Khan's life, the young Altaaf runs away and is found and brought up by a terrorist group led by their Pathan leader Hilal Kohistani, who brainwashes him into thinking that he and his men act according to Islamic principles and trains him to become a terrorist.

Ten years later, Hilal and an adult Altaaf are assigned the task of completing "Mission Kashmir", a plan of an unnamed terrorist sponsor that involves — or so Altaaf is told — killing the Indian Prime Minister. Hilal uses Altaaf's hatred as a means to achieve his own goals while encouraging the latter to target Khan, who is now an Inspector General, for his family's death. Altaaf visits his childhood friend and television personality Sufiya Parvez and, though he falls in love with her, uses her to try and make Hilal's plan of blowing up the local TV tower of Srinagar on Khan's birthday successful. He makes another unsuccessful attempt on Khan's life, which resulted him to be branded as a wanted criminal by the media and a fallout between Khan and Neelima.

At the same time, Sufiya learns of Altaaf's true occupation and breaks off her relationship with him. On the same date that Atlaaf's family was murdered, Altaaf makes another attempt on Khan by having three of Hilal's men plant a bomb in Khan's briefcase. Unfortunately, Neelima falls victim to it by accident, much to the complete distraught of both Khan and Altaaf, with the former having lost his chance to apologize for his argument with her and the latter screaming in remorseful agony for killing her.

Eventually, Khan manages to invade one of the terrorists' hideouts and discovers evidence and information about Mission Kashmir after capturing the bomb-briefcase men. After going through some cassette tapes with the help of Sufiya, Khan realized that the true goal of Mission Kashmir is to launch missiles on the local places of Hindu and Muslim worship to escalate Hindu-Muslim conflict across the subcontinent, thereby dividing Kashmir and turning it into a war zone. It also turns out that the attack on the TV tower was planned by Hilal to spread the rumor of assassinating the Prime Minister to cover up the true plot. Khan also realized that Hilal deliberately kept the true plot of Mission Kashmir as a secret from Altaaf for he feared that Altaaf would not support it; this was evident when Atlaaf leaves to the swampy hideouts to prepare for the launches, Hilal secretly tells one of his men to keep an eye on Atlaaf and kill him if he doesn't consent over the true targets.

By staging a fire in the jail that allows one of the bomb-briefcase men to escape, Khan and his men manage to track down and capture Hilal. Khan offers to make a deal with Hilal: going under the false pretense of allowing Hilal and his men to continue forward with Mission Kashmir in exchange for killing Altaaf to avenge Neelima's death. Seeing that Khan's 'hatred' of Altaaf is worthy of a Pathan's duty, Hilal accepts the deal, and to ensure no other mistake will be made, Khan goes alone with Hilal to the hideouts.

As Hilal and Khan reach the hideouts, Hilal tells Altaaf of Khan's whereabouts. An enraged Altaaf starts beating up a weary Khan, but the latter reveals to him the true goals of Mission Kashmir, stating that Kashmir will be turned into a hell if he lets Hilal destroy the holy shrines. Hilal orders Altaaf to shoot Khan, who is willing to accept his fate after expressing his dear love for Altaaf and remorse for killing his family.

As Altaaf struggles to do it, he remembers that Neelima took him to the shrines and the comment Neelima said about choosing sides during her visit earlier. Unwilling to betray his mother, Atlaaf decides to put his plan of revenge aside and aids Khan in stopping Hilal and his men from targeting the holy shrines. However, Hilal throws a bomb to distract them before getting shot to death by Altaaf, giving Hilal's men a chance to prepare to blow up the shrines.

While Khan shoots down several terrorists, Altaaf redeems himself by taking possession of a missile launcher and using it to destroy the other launchers and kill the remaining terrorists, thus saving the shrines. However, Altaaf gets shot in the torso and falls into the swamps. Khan jumps in and rescues the unconscious Altaaf by bringing him to shore, evading the explosion of the hideouts caused by Altaaf's act of redemption.

The plans of Mission Kashmir are revealed to the public by the media, and the terrorist sponsor's hideout is found by Kashmiri police, who shoot the sponsor as he tries to get away after killing two of his associates. Altaaf wakes up from a pleasant dream, where he reconciles with Sufiya and forgives Khan, accepting the latter as his father again after 10 years.

• Hrithik Roshan ... Altaaf Khan
• Preity Zinta ... Sufiya Parvez
• Jackie Shroff ... Hilal Kohistani
• Sonali Kulkarni ... Neelima Khan
• Sanjay Dutt ... Inayat Khan
• Puru Raajkumar ... Malik Ul Khan
• Abhay Chopra ... Avinash Mattoo
• Vineet Sharma ... Gurdeep Singh
• Rajendra Gupta ... Chief Secretary
• Ashok Banthia ... Sharafat
• Mohsin Memon ... Young Altaaf
• Heenaa Biswas ... Young Sufi
• Yogin Soni ... Irfaan
• Rohit Dua ... Goru
• Suchita Trivedi as Dr Akhtar's wife

Security is always tight in Kashmir, due to the very real threat of terrorist violence. Hence the inspiration for films such as Mission Kashmir which address the local militant insurgency in Jammu and Kashmir and the broader Kashmir conflict between India and Pakistan.

But in late 1999 when young lead actor Hrithik Roshan arrived on location to start shooting Mission Kashmir, his first film had not yet released to theatres, so no one recognized his face. Arriving for the first day's shoot in Srinagar dressed as a Kashmiri militant, which he portrays in the film, the security guards on location thought Hrithik really WAS Kashmiri - because of his fair skin and light colouring - and refused to allow him on set! Shortly thereafter, on 14 Jan 2000 Hrithik's début film Kaho Naa... Pyaar Hai turned him superstar overnight, 'Hrithikmania' swept India ... and his face was instantly recognized everywhere.

Mission Kashmir received generally positive reviews from critics. Mohammad Ali Ikram of Planet Bollywood gave it an 8.5/10 rating, praising the film's technical quality and the lead actors' performances. Saisuresh Sivaswamy of Rediff.com wrote, "This is a story from the director's heart, not his head, and the sincerity comes across in frame after frame." Giving the film 4 out of 5 stars, N K Deoshi of apunkachoice.com wrote, "Beneath all the drama that goes on in the movie there lurks the aspiration to get across to people the message of what actually people of Kashmir are going through."^[5] Savitha Padmanabhan of The Hindu stated, ""Mission Kashmir" might have its faults but it is definitely a cut above the rest of the commercial Hindi films that have been made on terrorism." She also praised the cast's performance and the film's production values.^[6] Film journal Screen praised the performances, but further wrote, "Chopra makes a sincere effort in his latest film Mission Kashmir to bring to the fore, the turmoil in the valley. But one feels disappointed, all the same, that there is very little of Kashmiriyat in the story, which is more of a personal conflict between the victim of a police shoot-out and a police officer."^[7]

The soundtrack of the film contains seven songs. The music is conducted by the award-winning trio Shankar-Ehsaan-Loy, performing separately. Ehsaan Noorani composed three songs, while Shankar Mahadevan and Loy Mendonsa composed two songs each. According to the Indian trade website Box Office India, with around 15,00,000 units sold, this film's soundtrack album was the year's twelfth highest-selling.^[8]