Y: The Last Man

On July 17, 2002, all living mammals with a Y chromosome—including embryos and sperm—simultaneously die, with the exception of a young amateur escape artist named Yorick Brown and his capuchin monkey, Ampersand. Many women die as a secondary effect of male deaths, such as plane crashes. Society is plunged into chaos as infrastructures collapse, and the surviving women everywhere try to cope with the loss of men, and the belief that, barring a rapid, major scientific breakthrough or other extraordinary event, humanity is doomed to extinction.
Yorick's mother, a member of the U.S. House of Representatives, commissions Agent 355 of the secret Culper Ring organization to protect Yorick. The two travel to meet geneticist and cloning expert Dr. Allison Mann, who works to discover why Yorick survived and find a way to save humankind. Due to damage at Mann's laboratory in Boston, the trio first travel across the country to Mann's other lab in San Francisco, then to Australia and Japan.
During the trip, the group is chased by multiple parties who know of Yorick's existence and want to capture or kill him for their own purposes, including an Israeli army commando named Alter, the militant Daughters of the Amazon, and a ninja. They are aided by Yorick's sister, Hero, a Russian soldier named Natalya, an astronaut named Ciba, a former flight attendant named Beth who becomes pregnant after a one-night stand with Yorick, and Rose, an Australian sailor.
In China, the group learns Mann's father, Dr. Matsumori, is also still alive and has created many clones of Allison Mann. He reveals to Yorick that Ampersand had been one of his lab animals he was experimenting on. He believes Ampersand had been inadvertently shielded by what killed off other Y-chromosome lifeforms as a result of one of his experiments and that this protection was transferred to Yorick via pathogens. He also reveals that Ampersand ended up in Yorick's care by accident. When Mann learns that Matsumori plans to murder Yorick before committing suicide, she kills him. Armed with the samples and information she needs, Mann stays in China to work on cloning.
Yorick and Agent 355 journey to Paris, France, where Yorick is reunited with his ex-girlfriend, whom he wanted to marry before the die-off. After initially celebrating their reconnection, Yorick realizes he actually loves 355. After meeting up with 355, Yorick tells her how he feels and she reveals she feels the same for him. Agent 355 is killed shortly thereafter by Alter, using a sniper rifle. When Alter attempts to capture Yorick, he defeats her and says he believes her dedicated pursuit of him was actually a roundabout way of suicide. He lets her live, and she is remanded into the custody of the Israelis. Yorick and Beth soon become a couple and raise their daughter together.
Decades later, Dr. Mann has succeeded in cloning Yorick seventeen times, along with thousands of copies of a small number of deceased males. Most of the world enjoys peace and prosperity as economic and technological development has resumed. Yorick and Beth's daughter is President of France. Yorick is institutionalized after making a joke interpreted as a suicide attempt. He is visited by one of his clones, who is the same age he was during the die-off event. After imparting advice to his clone, Yorick escapes.