The clan is lured into a trap by John Castaway and the Quarrymen, where it is believed all but Angela and Bronx were killed in an explosion. Luckily, it is revealed Xanatos saved the Manhattan clan by predicting John's plan and bribing the builder of the trap to build a secondary one within to save them, though they remain hidden. Captured, Angela and Bronx are sent on a train to be put in proper captivity. However, the Quarrymen attack the train, speeding it up and planning to send it and the passengers onboard over a now-destroyed bridge. The public now sees the Quarrymen are insane, and are even more shocked when the Manhattan Clan come to save the train and capture the Quarrymen. The episode comes to an end with Goliath repeating the Season 2 narration, but ends with how his clan is now slowly being accepted by the world at last.
As the Manhattan Clan are finishing up their patrols and preparing to return to Castle Wyvern and the Eyrie Building, they hear the sound of a young child calling for help from a construction site and go to investigate. However, they discover that the child was nothing more than a recording, and they had been lured into a trap. Worse, they don't have time to escape as the sun rises, turning them to stone. Angela and Bronx, who were on a separate patrol arrive too late to help as they turn to stone and crash to the ground, thankfully not being damaged, but the construction site is then blown up by explosives planted beforehand, burying the Manhattan Clan under rubble.
When Elisa arrives later, she finds what appears to be the remains of Goliath and the others and is devastated. Angela and Bronx are loaded into a police wagon, and Elisa learns that Assistant District Attorney Margot Yale intends to press charges against Angela and Bronx for all the trouble they've caused Manhattan since being exposed. Despite her best attempts to defend them, Elisa is unable to sway Margot's mind. When she speaks to Xanatos sometime later, Xanatos reveals to Elisa that Goliath and the others are still alive, revealing that the trap had been made by Castaway and his Quarrymen to destroy the Manhattan Clan, but Xanatos was able to bribe the workers hired by the Quarrymen to install a secret turnstile that rotated the Manhattan Clan into a secure area where they were protected from Castaway's explosives, replacing them with rubble to make it look like they had been destroyed in the eyes of the public.
Once Goliath and the others awaken, Elisa reveals what's happened to Angela and Bronx, and the Manhattan Clan decide to pursue the train that will be carrying Elisa, Yale, Angela, and Bronx into upstate New York to a maximum-security facility where Angela and Bronx will be incarcerated. During the trip, Elisa again tries to reason with Margot, but Margot threatens to have Elisa stripped of her shield and dismissed from the NYPD if she continues to defend the Gargoyles.
However, the train is soon attacked by Castaway and his Quarrymen, intending to take out Angela and Bronx, along with all the passengers on-board to leave no witnesses. When Margot sees this, she soon begins to realize that her belief in the Gargoyles being dangerous were very well-misplaced when the Manhattan Clan arrives to protect the train and its passengers from the Quarrymen. At one point, Broadway arrives to help Angela, but both are knocked out by the Quarrymen. Margot is left shocked by their heroism, and the passengers soon offer to help them out as one of them, a doctor, comes over to help Elisa treat their injuries.
Goliath confronts Castaway in the locomotive, but Castaway pushes the throttle to full power before shooting and destroying the console, while having detonated explosives on the trestle bridge ahead to cause it to collapse, leaving the train on a course for a fatal crash. Goliath is able to overpower and knock Castaway unconscious, while smashing the coupling connecting the locomotive to the cars to pieces, leaving the locomotive to plunge off the destroyed bridge and explode, while using the jetpacks they stole from several Quarrymen, Hudson, Brooklyn, and Lexington are able to stop the rest of the train by using the thrust in the jetpacks as retro-rockets to slow it to a stop, saving everyone on the train.
Sometime later, emergency services arrive at where the train was stopped, and as Castaway is handcuffed and taken into custody, Margot goes before the press to announce that she is dropping all charges against the Manhattan Clan after witnessing their heroism first-hand with protecting humanity, just as they had done 1,000 years ago. As the sun rises, Goliath narrates that it is a new beginning for his kind as the episode, and the animated series, comes to an end.
- This is the final episode of the Gargoyles.
- In this episode, the Gargoyles are finally accepted by the world