The Ministry of Utmost Happiness opens by introducing Aftab, one of the main characters. Arundhati Roy writes:

She was the fourth of five children, born on a cold January night, by lamplight (power cut), in Shahjahanabad, the walled city of Delhi. Ahlam Baji, the midwife who delivered her and put her in her mother’s arms wrapped in two shawls, said, “It’s a boy.” Given the circumstances, her error was understandable.

[. . .] The next morning, when the sun was up and the room nice and warm, she unswaddled little Aftab. She explored his tiny body—eyes nose head neck armpits fingers toes—with sated, unhurried delight. That was when she discovered, nestling underneath his boy-parts, a small, unformed, but undoubtedly girl-part.

This unexpected anatomy charts the course of Aftab's life. She changes her name to Anjum and lives as a woman. She lives in a graveyard in a house where anyone who is shunned or mocked can come and find some kind of peace. She's driven to do this because of the treatment she experienced when people found out that she had both types of sex organs.

The book also discusses the violence in the Kashmir Valley which some of the characters get caught up in. People are murders -- including Musa's wife and daughter. Roy writes:

In this way the insurrection began. Death was everywhere. Death was everything. Career. Desire. Dream. Poetry. Love. Youth itself. Dying became just another way of living. Graveyards sprang up in parks and meadows, by streams and rivers, in fields and forest glades. Tombstones grew out of the ground like young children’s teeth. Every village, every locality, had its own graveyard. The ones that didn’t grew anxious about being seen as collaborators. In remote border areas, near the Line of Control, the speed and regularity with which the bodies turned up, and the condition some of them were in, wasn’t easy to cope with. Some were delivered in sacks, some in small polythene bags, just pieces of flesh, some hair and teeth.

This violence affects all the characters who surround Tilo, the other main character. They're people who fight for freedom and are often guided by the violence they cause. Many characters lose people in their lives to the violence and are never the same again after. This losing of themselves and their increased desensitization to what's happening around them is evident. For Tilo, it makes her want to be a mother.

New life invigorates many of the characters when they adopt Miss Jebeen the Second, named after Musa's dead daughter. Roy writes:

Miss Jebeen the Second was passed from arm to arm, hugged, kissed and overfed. In this way she embarked on her brand-new life in a place similar to, and yet a world apart from where, over eighteen years ago, her young ancestor Miss Jebeen the First had ended hers.

She grows up in the graveyard with Anjum and the other people who have been mistreated by society. Miss Jebeen is happy there. Roy says she is spoiled rotten by those who live there. Through her, some of the characters are able to heal the wounds of their pasts and look forward to brighter futures.