During the early 1930s in Chicago, the transcontinental train, Flying Pussyfoot, is starting its legendary journey that will leave a trail of blood all over the country. At the same time in New York, the ambitious scientist Szilard and his unwilling aide Ennis are looking for missing bottles of the immortality elixir. In addition, a war between the mafia groups is getting worse. On board the Advena Avis, in 1711, alchemists are about to learn the price of immortality. Based on the award-winning light novels of the same name, Baccano! follows several events that initially seem unrelated, both in time and place, but are part of a much bigger story—one of alchemy, survival, and immortality. Merging these events together are the kindhearted would-be thieves, Isaac and Miria, connecting various people, all of them with their own hidden ambitions and agendas, and creating lifelong bonds and consequences for everyone involved.

In the newly formed Shiniki district of Tokyo, Zen Seizaki is a diligent public prosecutor at the Tokyo District Public Prosecutors Office. Assigned to a case involving false advertisement, Zen—along with his assistant officer, Atsuhiko Fumio—investigate Japan Supiri, a pharmaceutical company that had provided fabricated clinical research on the company's new drug. While investigating the file of Shin Inaba, an anesthesiologist connected to the crime, the case takes a dark turn when Zen finds a page stained with a mixture of blood, hair and skin, along with the letter F scribbled all across the sheet. As he investigates further, the case goes beyond Zen's imagination and becomes vastly complex, challenging his sense of justice and his knowledge of the truth. Digging deeper into the investigation, Zen begins to uncover a concealed plot behind the ongoing mayoral election and ties to many people of interest involved in the election and those closer than he thinks. The case grows more severe and propels Zen into an unforeseen hurricane of corruption and deceit behind the election, the establishment of the Shiniki district, and the mysterious woman associated with it all.

Hidden in the backstreets of the Ginza district is Eden Hall, a lone bar operated by Ryuu Sasakura, the prodigy bartender who is said to mix the most incredible cocktails anyone has ever tasted. However, not just anyone can find Eden Hall; rather, it is Eden Hall that must find those who need it. Customers of varying backgrounds, each plagued with their own troubles, wander into this bar. Nevertheless, Ryuu always knows the ideal cocktail to console and guide each distraught soul.

For centuries, the Iga and Kouga ninja clans have engaged in a bitter war. But when a ceasefire is ordered by the powerful warlord Ieyasu Tokugawa, the two clans are forced to put down their arms. Years later, Gennosuke Kouga, heir of the Kouga clan, and Oboro Iga, heir of the Iga clan, have fallen in love. Through marriage, both heirs aim to bring peace to the clans. But their hopes are dashed when flames of rivalry between their clans are reignited, and they are dragged into another war. Ieyasu's two grandsons have both claimed to be the next heir to the shogunate. To resolve this dispute, both the Kouga and Iga are ordered to send their 10 best warriors to fight in a bloody battle royale, with each clan representing one of the potential shogunate heirs. Two scrolls with the names of the fighters are given and are to be marked in blood upon the given fighter's death. The prize for winning is the favor of the Tokugawa shogunate for a thousand years. Torn between their love for each other and duty to their clans, Gennosuke and Oboro must ultimately decide the fate of their clans.