Catherine reaches Vincent in the catacomb and rescues Vincent from his madness. However, as Vincent begins to recover, he realizes he has lost his bond with Catherine and is unable to sense when she is in danger. Meanwhile, a deadly explosion lands Joe in the hospital where Catherine discovers that she is pregnant and debates how to tell Vincent, but as Catherine begins investigating the explosion it leads to her being kidnapped by a powerful crime syndicate led by a shadowy figure.
Following Catherine's death on the rooftop, Vincent takes her back to her apartment and leaves her on her bed. Later, as Vincent is grieving, Joe begins an investigation into Catherine's murder, hiring a private detective Diana Bennett, who encounters Elliot Burch and also members of the Tunnel World at Catherine's funeral. Meanwhile, Vincent's past demons re-surface as well as memories of Catherine who soon begins to search for his son.
Vincent has begun his quest to find his 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 and Elliot discovers the role Moreno played in Catherine's death which leads to a confrontation resulting in Vincent being shot.
The man who killed Catherine and took her baby sends an assassin to get Vincent. He manages to find the underground world and goes looking for him. Vincent upon learning of his presence tries to lead him away from the others.
Not wanting to put the Tunnel World in further danger, Vincent decides to leave the tunnels and with the death of Snow, Gabriel plots for Vincent's demise. Meanwhile, Elliot is on the verge of financial ruin and Gabriel promises him he will restore his empire if Elliot were to betray Vincent. Diana reveals what she has found to Joe and later she stakes out Catherine's grave where she encounters Vincent who is in critical condition following an explosion on the docks that may have cost Elliot his life.
In the aftermath of the boat explosion that most likely killed Elliot, Diana is shocked when she encounters a wounded Vincent who collapses on Catherine's grave. She takes him back to her apartment where she nurses him back to health and they soon connect, with Vincent telling her about Gabriel. Meanwhile, Father comes above fearing Vincent has died in the explosion and seeks information from Joe.
After Vincent entrusts Snow's ring to Diana, she quickly discovers Gabriel's henchman have targeted her and soon kidnap her and take her to Gabriel. Meanwhile, Vincent's son has fallen ill and Gabriel convinces Diana to have Vincent surrender to him. Feeling that his son is slowly dying, Vincent surrenders and Gabriel quickly has him locked in a cage but allows him to meet his son for the first time.
With Vincent caged, Gabriel allows him to see his infant son who suddenly begins to make a miraculous recovery. Meanwhile, Diana is pursued once again by Gabriel's henchman but she manages to contact Joe with a lead that ultimately leads them to Gabriel's home in Staten Island. However, they may just be too late, as Gabriel has decided to kill the baby.
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. Diana offers Vincent a hand in his quest to find his son while Joe orders Diana to tell him all the information she knows about Vincent.
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."