Though Lovers Be Lost, Part 1 Catherine and the rest of the underdwellers become worried when they find Vincent in a delirious state, ready to rip up even Catherine. After he awakens, we find out Vincent has amnesia and doesn't remember anyone or anything, except his love for Catherine. Meanwhile, Joe gets injured in a blast intended for an old friend because of a black book with info on a mysterious kingpin. After Catherine gets the book she is informed by a nurse that she is pregnant. We find out later that Vincent no longer has the psychic link with Catherine and the amnesia is being caused by the child, with whom he will later be linked. Catherine needs help with the black book and goes to Elliot for help. Catherine's boss finds out and helps the mysterious kingpin, with whom he is in league, kidnap her. Meanwhile, Vincent is sure something is wrong but cannot feel anything through their link and Father puts out an alert with the underdwellers.
Though Lovers Be Lost, Part 2 Vincent and the underdwellers are still looking for Catherine, as is Joe. We see a mysterious stranger performing some action and later that evening we see the doctor who is taking care of Catherine. Catherine uses some of the pipes in the warehouse to signal the underdwellers. Vincent comes running, rips the warehouse asunder, and escapes with Catherine, but not before the mysterious kingpin sees Vincent. Six months later Elliot Birch is still looking for Catherine and receives a warning to drop his investigation. Joe is also told to back off as well. The stranger becomes obsessed with Vincent and his child and wants to claim it as him own. As Catherine's labor begins, the empathic link between the lovers is re-established and Vincent comes running, but the link is actually between Vincent and the baby. As Vincent rushes through the building to find Catherine, the baby is born and the kingpin takes off with the child and orders the doctor to kill Catherine. Vincent makes it to the heli-pad only to see the face of the kingpin as the helicopter flies off. As he turns around, he finds Catherine, who has crawled to the roof to find her child. She tells Vincent there was a child and then dies in his arms.
Walk Slowly Catherine is gone and after Vincent carries her dead body to her high rise apartment and lays her in her bed, he sits with her till dawn, when he sheds a tear. He makes an oath that "while I live, you live...with me... in me ...always... always." Joe wants to find out who the killer is and brings in a woman named Diana Bennet, who is reported to be a phenomenal detective who gets to pick and choose her own cases. Meanwhile, Vincent mourns and everyone who knew Catherine deals with her death in their own way. Diana Bennet begins her investigation. In a vision Vincent realizes that Catherine has left him a child. Father attends Catherine's funeral in Vincent's place.
Nevermore Vincent goes back to the place where Catherine died to get an idea of where his son is, but decides he will seek the help of Elliot Birch. Meanwhile, Diana continues her investigation. Elliot's empire is starting to crumble because of the black book and the investigation of Catherine's disappearance and murder. Elliot goes to see Joe to enlist his help in finding Catherine's killer, but he balks. After more pushing by Elliot, his security officer is killed and left as another message for Birch to back off. Diana finds Catherine's basement entrance to the underground. Joe goes to see Birch and tells him he knows that Moreno (the D.A.) is on the take. The kingpin tells Moreno to take care of the problem, so he sets up Birch for a hit, and Vincent stops him, but not before he shoots him.
Beggar's Comet Elliot receives a message to meet with Vincent. Vincent reveals the name of the mysterious kingpin and his name is Gabriel. He found out the name from Snow, the assassin (and brother to Gabriel), whom Gabriel sent to kill him last episode. He asked that Elliot continue to dig into Gabriel's dealings, and he agreed. Gabriel is brought the body of Snow. Gabriel shows no remorse, but is upset when he does not find their father's ring on the body and orders his minions to find it. Joe has taken over Mareno's job as district attorney. He questions Elliot's bodyguard about Mareno's death and puts out a search warrant for Elliot's clothes, but Diana doesn't believe him guilty because of the condition Mareno's body, which was sliced and diced.Joe doesn't care, so Diana asks him to her loft to show him evidence he needs to see. The underdwellers hold a funeral for those who were killed during Snow's killing rampage. Elliot is told that his fight is over and that he needs to file for chapter 11 bankruptcy. Diana shows up and asks Elliot to tell her everything that happened that night at the carousel when Moreno died, and also who is Vincent. Vincent is depressed because of the deaths he believes are his fault because Snow came into the underground for him. Vincent decides to leave the underground shelter to protect everyone. Joe arrests Elliot for Moreno's murder. Diana tells Joe that the person who killed Catherine is not the same person who brought her home. The person who brought her home was Vincent and he loved Catherine. She shows him the pictures of the victims and postulates that they were sliced and diced by an animal. She knows that there are tunnels under the city and that Vincent somehow knew when Catherine was in trouble and came to her aid. Elliot is mysteriously released and Gabriel's lieutenant shows up to take him to meet with Gabriel, uncertain whether he will live out the night he acquiesces. Gabriel tells Elliot that the war was over and that he was finished and that he killed Catherine, but wouldn't have, had he known how much trouble it would have been. He tries to turn Elliot against Vincent by pointing out that Catherine never loved him, that she loved Vincent and it was Vincent that took Catherine away from him, not he. He offers to give it all back to him, or death. Elliot breaks and decides to turn Judas for his 20 pieces of silver, so he sets up Vincent to be shot, but at the last moment he changes his mind and tells Vincent to flee and sacrifices his life to the sniper while Gabriel looks on in his video monitors. Gabriel is disappointed in Elliot, even though he was going to kill him anyway. He orders his henchmen to blow up the meeting place with the explosives he had placed there as a contingency. He looks on with glee as believes he has killed Vincent. The explosion causes a blackout in the city, and Gabriel gloats to Vincent's son that it's over and he is safe. Vincent survives the blast, but believing he is at his last moments struggles his way to Catherine's grave where he collapses in front of Diana who has all her suspicions confirmed as she sees his face.
The Chimes At Midnight Vincent has a waking dream of a hooded character who is stalking him while a baby cries, and Diana is trying to find out more about who Gabriel is by his ring. She believes Gabriel has sent masked killers to break into Diana's loft apartment, but Diana hears them and makes her way to the roof where she uses their very equipment to make her escape. She is spotted and runs for her life. She almost manages to get away, but the men use a hostage that they threaten to kill if she doesn't come peacefully. Vincent talks to Father and tells him of his dreams and possibly the return of his empathic powers. He also tells that he has become involved with another woman (Diana), although not necessary romantically. Diana is brought before Gabriel who shows her his son, Vincent's son. Catherine's child is dying and needs his natural father. It is the truth, but also obviously a trap for Vincent. They let Diana go so she can tell Vincent and he decides to go into the trap anyway to save his son. Every part of his waking dream comes true and Vincent awakes in chains and an electrified cell. Gabriel watches Vincent in his cell and hopes that just the close presence of Vincent will heal the child, but it is not so. Gabriel will not let the child near Vincent. Gabriel relents and has the child brought to Vincent, and we finally see that the child looks normal like Mom and not like Pop.