Witness descriptions of a subway vigilante lead Catherine to believe that Vincent may be responsible.

Upon being injured in an explosion, a half-blind Vincent is captured by a vicious street gang. Catherine with the help of her self-defense teacher Isaac are out to find Vincent.

After Vincent is accidentally caught on film. he is captured by two men. One of them, Dr. Edward Hughes, is a scientist who is desperate to learn the truth about Vincent. The other man, graduate student Jonathan Gould, believes Vincent is a freak of nature, and wants to reveal him to the public and become famous. However, Hughes finds out that Vincent is capable of speech and learns of the awful pain that Vincent is going through from being caged. Catherine finds the tranquilizer darts used when Hughes and Gould captured Vincent and tracks down Dr Hughes at his office.

Catherine learns that a city's model, Ridley Foster Home, holds a dark secret: selling orphaned children to criminals, who force them to pick pockets. She saves one such orphan, Eric, and brings him to "The World Below" where he's welcomed by Father—who promises his missing sister Ellie a similar refuge—while Vincent helps Catherine find Ellie and end the child-selling racket.

Upon witnessing a shooting, deaf Laura Williams (Terrylene) must decide if she should leave the sanctuary of "The World Below" to free an innocent man. While Catherine is investigating the same case, Catherine is beaten up in her apartment by the men who were behind the murder. After receiving loving assurance from Vincent and Catherine, Laura bravely gives her statement to the police.

Chinatown is the setting of a "Romeo and Juliet"-like story of a woman who is friends with Vincent and who has fallen in love with one man, but—through an arranged marriage—has become engaged to the son of a Triad leader.

Vincent has foreboding dreams when Catherine's former fiancé Steven Bass returns to her life, and with good reason: Catherine is barely aware Steven—whose parents are now dead, who's dying of brain disease, but whose becalmed manner at first belies that he's still a control freak—is obsessed with making her the wife she doesn't want to be to him, and goes to a pair of troubling extremes to make it happen.

A necklace Mouse gives Catherine as a gift turns out to be made of antique gold, found in a buried ship Mouse discovered by accident deep in "The World Below." When he shows Winslow and Cullen, it leads to an unheard-of spell of raw greed among their fellow tunnel dwellers, especially when Cullen tries to claim the ship's treasure as his own for sale, until Catherine, Vincent, and Father find a surprising resolution.

Vincent and Catherine become involved with a gypsy boy who's been banished from his tribe because of a crime his father was supposed to have committed and who claims that his father was actually innocent.

Catherine receives an unexpected visitor on her balcony: Paracelsus's minion Erlik, who captures Catherine in a plot to lure Vincent to the lower parts of "The World Below" and kill him so that Paracelsus can overthrow Father and take over "The World Below". Despite knowing what Paracelsus would do, Vincent goes to rescue her with the help of Pascal, Winslow, and Jamie.

Vincent rescues a man named Dimitri Benko from drowning and brings him to "The World Below" to recuperate. Little does anyone know, Dimitri is carrying the pneumonic plague which soon becomes an epidemic amongst the residents of the tunnels and begins taking lives. Meanwhile, Catherine discovers that Dr. Peter Alcroft is an old friend of Father when it comes to helping the infected.

When "The World Below" is planning an annual winter event called Winterfest with Catherine and the other "Helpers," Paracelsus plans to crash the party. Catherine and Vincent suspect that someone at the party is actually Paracelsus in disguise and must find out who it is.

Catherine convinces Vincent and Father to welcome pregnant former prostitute Lena to the "World Below" where she can have her baby and be part of the community, but a crush on Vincent turns to more for Lena after her baby is born. After running away when Vincent rejects her advances gently but firmly, Lena is found by Catherine, who convinces her to return to the tunnels, where she names her baby after Catherine.

Deaf Laura Williams (Terrylene Sacchetti) now lives in surface New York but backs away as a helper for "The World Below" when she falls in with a gang of young, angry deaf people whose leader, Lincoln, is investigated for a security guard's murder. Laura's boyfriend in the gang, Jerry, is an undercover police officer who reveals his secret to her, prompting her to run away. She returns to discover Jerry's cover blown and the gang sentences him to a punishment "sticks and stones." He is rescued by Catherine and the police who are searching for him, as well as Vincent who is summoned by one of the helpers.

Devin Wells returns to "The World Below" with Charles, a deformed man with Proteus syndrome who seeks sanctuary from his abusive brother Eddie while escaping from a carnival where he's billed "The Dragon Man." Vincent befriends Charles but the deformed man's fear and awkwardness lead to complications until Devin agrees to care for Charles at a mountain retreat.

A resident of "The World Below" named Kanin—about to celebrate his first wedding anniversary below—is recognised by a woman in "The World Above" as the driver who killed her small son in an accident sixteen years ago, the real reason Kanin retreated to the tunnels. Catherine discovers his warrant by accident and doesn't want to force Kanin to leave his family, but Vincent convinces him to face his responsibility and give closure to the still-grieving woman.

When Catherine's father dies of a stroke, she retreats to "The World Below" to grieve. She asks Vincent to let her stay with him and not return to "The World Above" and though he agrees, he knows that eventually she will need to go back. One night she is visited by her father's spirit in a dream and she comes to terms with losing him, which gives her the strength to return to her world.

Former "World Below" resident Lisa Campbell – now a world-famous ballerina — returns to the tunnels for refuge, desperate not to testify against her controlling and arms-running boyfriend. Her return unnerves Vincent—who loved her when they were teenagers, but who injured her once during an embrace, a major reason he fears physical intimacy with Catherine. But Catherine consoles Vincent and convinces Lisa to face the authorities and do what she can to put her boyfriend away for his crimes.

The CIA pushes Catherine and Joe off investigating the murder of an old man who proves to be the father of Elliot Burch—whose shady dealings in Central America have him in danger from a country's death squad, leading Catherine to put her own life on the line to help him.

Catherine is attacked by two men in the park who are disguised as police officers. Vincent comes to her rescue only for it to be a set-up caused by a shadowy figure who has hired an investigative reporter named Bernie Spirko to expose Vincent's existence to the public at large.

Vincent is haunted by dreams of heavily-snowing winter, and no wonder: Gabriel sends an assassin named Snow to eliminate him, leading him to lead Snow away from the "World Below" inhabitants when Snow finds the tunnels. Meanwhile, Joe has become acting district attorney in the wake of Moreno's exposure and murder and is free to continue his own investigation. Snow dies in a cave-in in the deepest tunnel.

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.

Guest star: Suzie Plakson as Susan, Miguel Sandoval as Jerry

In the aftermath of Gabriel's death, Vincent introduces Diana to the inhabitants of "The World Below." When Father receives a visit from his old flame Jessica Webb, it prompts Mary (Ellen Geer) to confess to Vincent that she's been in love with Father a very long time. Diana investigates the strange murders of ex-inhabitants turned helpers of "The World Below"—all of whose faces are covered in blue ash.

Father says a painful goodbye to Jessica, who can't let herself return to "The World Below" while Father knows he must return. He returns to the tunnels and discovers former inhabitant Gregory Coyle has committed the murders—seeking 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 again but clashes with an old-school detective (John Pleshette), who refuses to believe her description of Gregory's pattern. Gregory buries Father alive in a little-used tunnel but lets himself fall to his own death despite Diana and Vincent's rescue attempt. The series concludes with Diana and Vincent in his chamber, and Diana holding Vincent's baby son next to him.