Taking place roughly 6 months after Claude Frollo's death, Quasimodo is shown having nightmares, ie. his old master's face looking cruelly down at him and clips from the first movie (such as Frollo's actual death and Frollo burning Esmeralda). He then wakes up in a puddle of sweat, he goes over to the gargoyles for consolation. But to his shock, they don't come to life. After a brief panic, they show slight instances of movement and then comfort him, telling him that Frollo is dead and can't hurt him.
The next day, while shopping in the town square, Quasimodo sees Frollo in various locations and places. After this day, Quasimodo decides to remain isolated in Notre Dame. But after several weeks of his nightmares and hallucinations, he notices that the gargoyles are no longer parts of his imagination, and cannot bring them to their states of being. Quasimodo shows genuine fear, and slowly retreats to his bed. Trying to isolate himself from the entire world, but after some brief flashes of Frollo's malice, he decides enough is enough.
He climbs up to the topmost gargoyle on the cathedral and is poised to jump off, ending it all.
However, he hears Esmeralda and Phoebus calling his name, and he is ecstatic; he hasn't seen them in weeks, since their honeymoon.
While having lunch with them, he seems to be pretty calm about the whole ordeal, but he looks up and sees Frollo at the head of the table. Startled, he jumps back, and trips over the rail. Laverne's hand happens to be open and catches him by the scruff of his shirt. After Phoebus and Esmeralda pull him up, he becomes emotionally unstable and more panic-stricken.
He looks over at the gargoyle which Frollo was stood on before his death (which has since been repaired), and notices that it has the Judge's face.
Esmeralda has Quasimodo admitted to a mental asylum, and he eventually comes to terms with the fact that Frollo is dead and won't come back.
So, as he goes back to Notre Dame, he notices a man, calling himself Jehan. He says he came to visit his brother, Claude, but can't seem to find him anywhere. After going to the top, Quasimodo tells Jehan that Claude was killed almost a year ago.
In a fit, Jehan pulls out his dagger, and is poised to kill Quasimodo. The latter kicks Jehan over, and runs up to the bells, where the gargoyles assist him, pointing out directions where he can escape. But Quasimodo realises he has to come to terms with his fears and lures Jehan up to the top of the cathedral. After Quasimodo restrains Jehan, he pulls away the dagger and throws it over the railing, Jehan reveals that was given to him by Claude, and was the only posession he had left of him, he then grabs Quasimodo and pushes him over the railing, Quasimodo manages to hold on, by grabbing the tongue of one of the overhanging gargoyles, he then pulls Jehan's foot forward, through the railing, and he slips over, Quasimodo then climbs over, to which Jehan punches him flat in the face, getting a large amount of blood coming out. Quasimodo looks at him full of wrath, he grabs him and it looks as though he's about to throw him over the railing. But he looks up and sees the fear in his face, he lowers him down, but realises his mistake, when Jehan grabs Quasimodo and pushes them both over the side, Quasimodo manages to grab hold of one of the lower down overhanging gargoyles, but Jehan plunges to his death. A crowd gather round his body and look up at Quasimodo. They then march into the cathedral, where the Archdeacon berates them for taking their anger out on an innocent man, claiming he saw the relent in Quasimodo's eyes. Clopin and some other gypsies, then also vouch for this, adding that Jehan was responsible for his own death, trying to kill Quasimodo too.
The crowd then realise how quick they were to judge and turn back, leaving Quasimodo alone.
The final shot shows Quasimodo asleep, with a smile on his face, his dreams contain Frollo surrounded by mist, to the point at which Frollo completely disappears.