After recovering from his violent madness, Vincent finds himself unable to sense when Catherine is in danger. When an explosion lands Joe in the hospital, Catherine learns that she is pregnant and ends up captured by a crime syndicate led by a shadowy figure during her investigation.
Vincent, Joe, and Elliot each continue to search for Catherine after she was kidnapped. As Catherine's pregnancy begins its final phase, Vincent detects his child's presence which leads him to a skyscraper where the crime syndicate's leader Gabriel has plans for the newborn child.
Following Catherine's murder at the hands of Gabriel, Vincent takes Catherine's body back to her apartment and leaves her body on her bed. Joe begins an investigation into finding Catherine's murderer and hires Diana Bennett to help him. Diana encounters Elliot Burch and members of "The World Below" at Catherine's funeral.
Vincent begins his quest to find his captive son and makes his first move by revealing himself to Elliot. Meanwhile, Diana has become immersed into Catherine's life and soon discovers the entrance into the Tunnel World in the basement of Catherine's apartment building. Elliot soon discovers District Attorney John Moreno's role in the death of Catherine.
Gabriel sends an assassin named Snow to eliminate Vincent. When Snow finds the entrance to "The World Below," Vincent must lead Snow away from its inhabitants.
Vincent plans to leave "The World Below" to keep its inhabitants from being targeted by Gabriel's men. Following the death of Snow, Gabriel plans to have Vincent killed and approaches Elliot with an offer to betray Vincent.
Following the boat explosion, Diana finds a wounded Vincent at Catherine's grave and takes him back to her apartment to heal. Father comes to the surface and visits Joe to know if Vincent had perished in the boat explosion.
When Vincent entrusts Snow's ring to Diana, she becomes a target for Gabriel's men and ends up captured. Vincent surrenders himself to Gabriel when he hears that his son is terminally ill.
With Vincent a prisoner of Gabriel, he witnesses his son making a miraculous recovery. Diana can't return to her apartment as it's under surveillance by Gabriel's men. Upon learning of Vincent's capture, Father and the other inhabitants of "The World Below" bring Diana to "The World Below" where she gives them the description of the floor tile in Gabriel's house.
Rolley is shot while trying to rob a liquor store and takes refuge in the tunnels. This brings his heroin addiction to the forefront and Vincent vows to do his best to help Rolley which leads to a fiery encounter at a drug house that unknown to Vincent is run by Gabriel.
In the aftermath of Gabriel's death, Vincent introduces Diana to the inhabitants of "The World Below" and attends the baby-naming ceremony of Vincent's son who names him Jacob after Father. When Father receives a visit from his old flame Jessica, Diana investigates the strange murders of ex-inhabitants of "The World Below."
Upon returning to "The World Below" upon the knowledge of some of ex-tunnel inhabitants being murdered, Father encounters Gregory Coyle who seeks revenge for the death of his father by cave-in 20 years ago. Diana makes it her mission to catch Gregory before he can kill another ex-inhabitant of "The World Below."