The birth of Gotham City is one shrouded in both mystery and mysticism. Millennia ago, an evil warlock was buried alive beneath what would one day become the central island of Gotham. It is alleged that while the warlock laid in a state of torpor, his evil essence seeped into the soil, poisoning the ground with his dark, corruptive touch. By the warlock's own reasoning, he claims that he fathered the modern spirit of Gotham City and has even taken to calling himself Doctor Gotham. 
The territory surrounding Doctor Gotham's burial spot was also the home of an ancient Native American tribe known as the Miagani. The Miagani inhabited the Gotham islands several centuries before European explorers ever crossed the Atlantic. The Miagani tribe is no longer in existence, and there is much speculation as to their final fate. One posited theory suggests that a shaman named Blackfire came to them, proclaiming to be a holy messenger. Within short order however, Blackfire took control of the Miagani and proved to be a cruel and evil tyrant. The Miagani chieftain Chief Paleface demanded that Blackfire leave the tribe, but the shaman would not be silenced, and he struck down Paleface with his staff, killing him. The other Miagani revolted against Blackfire. They shot him with their arrows and tied him to a pole to die. Blackfire didn't die though, so the Miagani sealed him inside of a cave. They erected a totem in front of the tomb as a warning sign of the evil that resided within. Some sources cite that Shaman Blackfire emerged from the cave and used his power to cause a blight across the land. As such, the Miagani had little choice but to abandon their homes in search of fertile ground. Two days into their journey, a rival tribe came upon them and slaughtered all of the Miagani. Some legends however, say that it was actually Shaman Blackfire who murdered them. 
In 1609, the Dutch East India Company selected English explorer Henry Hudson to chart an easterly passage to Asia. Along his journey, he surveyed the Northeastern coastal region of what would one day become the United States.  Following Hudson's course, Dutch pioneers sailed for this New World and began populating the region once inhabited by the Miagani. The pioneers established themselves in two different colonies. One colony was set up along the shore where fishing was plentiful, and the other was developed further inland. The latter colony came upon the sealed cave with the Miagani totem erected before it. Unaware of its significance, they ignored the totem's warning and loosed Shaman Blackfire from the cave. The colonists were never seen again. Two days later, men from the coastal community traveled to visit their inland brothers. When they arrived in the village, they found the town deserted. Pools of blood dotted the streets, but there were no bodies. A trapper claimed to have seen the image of a naked Indian walking from the woods to the settlement. 
During the latter half of the 18th century and the early half of the 19th century, Gotham was a major port city known as Gotham Town. Beginning as early as 1799, Darius Wayne began construction on a family estate that would eventually become known as Wayne Manor.
On January 1st, 1800, the frontiersman known as Tomahawk became embroiled in a fight with a British spy named Lord Shilling. Shilling had disguised himself as Tomahawk's close ally Stovepipe in order to get in close enough to procure a piece of mystical amber that Tomahawk had acquired from occultist Jason Blood years earlier. The two fought one another inside of an immense, bat-filled cavern not far from the Wayne estate. During the fight, the piece of amber fell into a stream of molten fluid. Shilling reached to retrieve it, and the amber fused itself to his hand, mummifying his entire arm. Tomahawk severed the arm and returned with it to Gotham Town. The arm and amber later became known as the Claw of Aelkhünd. The cavern in which the two fought one another would later service modern age super-hero Batman as the Batcave. 
During the 1950s, Gotham evolved with the changing times, particularly in light of the paranoia perpetuated by the Cold War. Various bomb shelters were erected all throughout the city. By the 1960s, Gotham City planners began an ambitious project called the Underground Highway. Beginning at Fourth Avenue, they began building an actual subterranean thoroughfare designed to link with the subway system. They only managed to complete two-hundred yards worth of tunnel before budget cuts forced them to abandon the project. In later years, the unfinished highway became a haven for the homeless and even a few criminals such as Killer Croc. 
Gotham City had suffered the results of a magnitude 7.6 earthquake in an event commonly referred to as the "Cataclysm". With hopes for rehabilitating the broken city, the United States government declared it a No Man's Land, which effectively quarantined the entire island city. Eventually, thanks in no small part to the financial and political machinations of Lex Luthor--dipping his hands, as ever, in both legitimate and illegal means to achieve his goals--Gotham City was released and rebuilt, and rejoined the United States.