The clan began as a group of gargoyles who initially hailed from Scotland centuries ago, during an era when humans and gargoyles held an uneasy peace.
The Vikings then captured many of Castle Wyvern's human inhabitants, as the surviving gargoyles followed to exact vengeance. They successfully rescued most of the castle's inhabitants; however, the Magus cast a spell on five of the gargoyles that turned them permanently to stone, believing that the gargoyles had caused the death of Princess Katharine during the counter-attack. However, when the Princess returned after being rescued by Goliath, the Magus realized that he had made a terrible mistake. Unfortunately, the necessary counter-spell was destroyed earlier when the Viking leader Hakon burned a page from the Magus' spellbook to taunt him, thus precluding restoring the clan, except for the fact that the curse would end when the castle "rose above the clouds," which seemed impossible at the time. A grief-stricken Goliath, feeling alone and wanting to join his brothers, asked the Magus to perform the spell on him while Katharine and the Magus would care for the rookery eggs.
One thousand years later, billionaire industrialist David Xanatos acting on a tip from Demona and the Grimorum Arcanorum that he owned, purchased Castle Wyvern and had it moved, brick by brick, to the top of his skyscraper, the Eyrie Building on Manhattan in New York City, New York. As Xanatos anticipated, the building was high enough to satisfy the requirement for the spell to be broken. This liberated the gargoyles from their stone sleep, only to be stunned to find themselves 1000 years in the future in a place far away from their ancestral homeland. After the initial shock passed, the clan would eventually attempt to fit in to their new environment with the five unnamed gargoyles (apart from Goliath), taking names from New York boroughs and landmarks to allow the people of this world to better relate to them. For the most part however, the period of adjustment was relatively smooth, for the younger trio in particular who delighted in the vast varieties of goods and activities available.
Despite being grateful for their release from their slumber, the new Manhattan Clan was reluctant to put their trust in another human. This was fortunate, as their benefactor David Xanatos intended to use them for his own Machiavellian schemes. Xanatos reunited Goliath with Demona, then used the gargoyles to steal information from a rival corporation. Instead of remaining without human contact, they befriended NYPD detective Elisa Maza, and were eventually forced out of their ancestral home of Castle Wyvern and into a Clock Tower above Elisa's precinct.
From their new home, they charged themselves with defending the island of Manhattan, as well from Xanatos and Demona, now their enemies who still wanted to dominate them. As they acclimated to the new home, the clan worked to reestablish their command structure, with Brooklyn appointed as Goliath's second after the elderly Hudson had stepped down from the role. Later on, Goliath, Elisa, and Bronx were called away to help the grown children of the Avalon Clan on the mystical island of Avalon where they met Goliath's daughter, Angela and the surviving rookery eggs. After defeating the threat, they were sent on a quest by Avalon to battle evil and correct wrongs worldwide with Angela accompanying them. In the meantime, Brooklyn had some initial difficulty assuming leadership of the clan, but soon developed into a better leader. The group returned to Manhattan with the new addition to the clan, but also with the hope that the gargoyle species is doing far better than they ever hoped with the discovery of numerous clans in existence worldwide.
Following the destruction of the clock tower, they moved back into their ancestral home at Castle Wyvern courtesy of a grateful Xanatos, who was thankful to the gargoyles for defending his family against threats towards them. Thanks to the Hunters, the general public, now aware of their existence, fears, and seeks to destroy them.
Around Halloween of 1996, Thailog stormed the Labyrinth, temporarily reclaiming control of the clones of the Manhattan Clan. Together, they crashed the Xanatos Halloween Masque, where Thailog collected genetic samples from each member of the Manhattan clan, including Elisa, Bronx, and Angela, and all the clones save Brentwood abandoned his company.
Shortly thereafter, Macbeth entreated the Manhattan clan to help protect the Stone of Destiny while it was transported to Scotland from England. Goliath, reluctant at first, allowed Lexington and Hudson to join Macbeth on his quest. Shortly before Hudson and Lexington returned with Coldstone and Coldfire, the Phoenix Gate appeared and swallowed Brooklyn. Though it seemed as if he were only gone for minutes, Brooklyn had been traveling through time for forty years, and returned with an entire family unit, and a new gargoyle beast.