The Second City was the place where the Antediluvians first gathered after the Biblical Deluge, trying to recreate the glory of the First City. The Second City was never granted a name and eventually collapsed under civil war.
After the Great Flood, the surviving members of the Third Generation (now the "Antediluvians") rose up en masse and destroyed their sires and sought dominion over what the Second Generation once had. At this time vampires were living on a rich diet of each other's vitae and Caine appeared one last time to curse each of the Antediluvians for their crimes of rebellion and hubris in striking down their own sires. From these curses come the weaknesses associated with each clan.
The Antediluvians tried to reassembled while the descendants of Noah spread across the earth. They built a new city, bringing to it thirteen tribes. It was a beautiful city and its people worshipped them as gods. The Antediluvians created new progeny of their own, the Fourth Generation of Cainites. But they feared the Jyhad, and it was forbidden for those childer to create others of their kind - this power the elders kept for themselves, and when a childe was created, it was hunted down and killed, and its sire with it.
Although this city was as great as Caine's Enoch, it eventually grew old. As do all living things, it slowly began to die. The "gods" at first did not see the truth, and when they last looked about them it was too late. The Second City was destroyed and their power extinguished, and they were forced to flee, their progeny along with them. But many were killed in the flight, for they had grown weak. With their authority gone, all were free to create their own broods.