The film opens with the revelation that violence has escalated in India, alarming all who know of its having done so. The focus then shifts to reveal the central villain, Mogambo. Two henchmen, Teja (Ajit Vachani) and Daaga (Sharat Saxena) arrive by chopper to report to Mogambo their progress in their subversive activities against India, which include selling weapons and armaments to terrorists and starting illegal gambling dens all over the country. Mogambo is portrayed as a brilliant yet insane General whose goal is to conquer India. He asserts his domination over his men by commanding three soldiers to leap into a pit filled with concentrated acid to certain death and utters, with satisfaction, his signature line Mogambo khush hua ("Mogambo is pleased"), when his lackeys obey his orders without question. This line was voted the best of its category. Its counterpart, Mogambo nahi khush hua ("Mogambo is not pleased") usually is a death sentence for his men.
The island of Mogambo is modeled after the island of Dr. No; it is a self-contained colony, having advanced communications, weapons, and laboratories to build various high-tech devices. Mogambo sits on his throne in the island, monitoring the evil perpetrated by his henchmen all over India and hoping to someday conquer India entirely. All his subordinates know the formal salute "Hail Mogambo!" (with an accompanying "Heil Hitler"-like gesture); this emphasizes his complete authority over his minions.
The film then introduces Arun Verma (Anil Kapoor), an orphan and a street-walking violinist who rents a large (mostly run-down) old house overlooking a beach. There he houses a dozen or so orphaned children, aged 5-12 approximately, who call him "Arun Bhaiyya" ("brother Arun"). He takes care of them with the help of his cook and caretaker Calendar (Satish Kaushik). Arun is generally poor, owes debts to the local food merchant Roopchand (Harish Patel), and is perpetually overdue to pay the landlord Maniklal (Yunus Parvez). In spite of these practical problems, Arun tries to look on the bright side of every situation and generally has fun with Calendar and the children.
As time goes by, Calendar gently reminds Arun that cost of running the home continues to rise and that they need to supplement Arun's meager takings as an ad-hoc violinist. Arun agrees and decides to rent out the sea-facing room on the first floor. When he goes to the local newspaper to run an advertisement for the room, he meets Seema Sohni (Sridevi); after an amusing incident between them, he makes her his tenant despite her reluctance to live in company of children.
When Seema ultimately discovers the children, she feels betrayed and gets angry; but when she sees Arun's plight and the nobility of his cause, she warms to them and eventually becomes friends with everyone.
The film undergoes a turning point when Arun suddenly receives a mysterious letter from a family friend, Dr. Sinha (Ashok Kumar), who reveals that Arun's late father had created a device that would make its user invisible.
With the directions in the letter, Arun, accompanied by his ward Jugal, enters his father's laboratory and finds the device. The device is in the shape of a large gold watch and worn on the wrist; when it is activated, it makes the wearer invisible to the naked eye. This invisibility is pervasive except for one flaw: when red light is focused on the wearer, he becomes visible. Thus, shining a red lamp on the subject, or viewing the subject through a red lens, makes the subject visible again.
Arun and Jugal decide to keep the device a secret between them. Around this time, Seema overhears a suspicious conversation on phone and goes to a lavish party hosted by Teja and Daaga. The party includes a cabaret-style song performed by Seema under the guise of a Hawahawaiian dancer. Her disguise is spoiled whereupon she is nearly killed by the criminals. Here, Arun invisibly rescues her, styling himself "Mr. India".
As a result of this, Seema discovers she is romantically attracted to her rescuer, though not to his civilian alter ego. She arranges to meet with him, and a dance ensues.. Because the gazebo in which they are courting is curtained by red curtains, Seema and the film's viewers can see Arun's silhouette through them, though he is wearing his invisibility and therefore cannot be seen when she looks at him directly.
Mr. India later defeats Mogambo's men in several encounters, foiling their criminal plans. Mogambo is enraged and intrigued by the "invisible man". One of his scientists, Mr. Fumanchu, informs him that they nearly acquired the invisibility-causing device when Dr. Verma invented it many years ago, but failed when Dr. Verma hid it and died without revealing its location.
Mogambo's computer-aided intelligence teams reveal that Mr. India's specific actions against the gambling den bring benefit to Arun Verma and his charges. Mogambo therefore has bombs disguised as toys and planted in places where children can find them. In total harmony with Mogambo's plan, one of the bombs kills Arun's youngest and dearest charge, Tina, driving Arun to immense grief. Later, Arun, Seema, Calendar, and the surviving children are brought before Mogambo.
Mogambo threatens and tortures them so that they may reveal Mr. India's true identity and the location of the invisibility device. Arun eventually volunteers this when Mogambo threatens to drop two children into the pit of concentrated acid; because Arun has dropped the invisibility bracelet, he cannot become invisible to prove himself. Frustrated, Mogambo orders the lot of them sent into the dungeons.
They all escape from the dungeons whereupon Calendar, and the children go one way, while Arun and Seema went another. Mogambo spitefully activates four gigantic missiles, which are poised to destroy all of India. Arun confronts him and the two fight. When Arun has overcome Mogambo, he deactivates the launch of the missiles, pausing to consider Mogambo's statement that preventing the launch would cause the missiles to explode on the spot. Arun, Seema, Calendar, and the children escape, while Mogambo's fortress is destroyed. Mogambo himself dies in the fire, uttering the phrase "Hail Mogambo!" as the flame engulfs him.
Arun's dual identity remains a secret to most people, while he returns to his former life.