ACT 1: New York City at night. A young man and woman are making out in a dark alley when an unknown assailant suddenly pulls the young man into the sewers through a nearby manhole, leaving the shocked young woman on her knees screaming for help.

ACT 2: The next day at the Daily Bugle, J. Jonah Jameson requests that Peter Parker (a.k.a. Spider-Man) and Betty Brant team up to get to the bottom of the recent disappearances; as well, if they manage to tie in Spider-Man into it, they get a bonus. A few minutes later, Peter and Betty are on their way to "save the city" when JJJ storms by them and tells them to see to it that they solve this mystery or else...A short time later, a limousine pulls up at the curb next to JJJ and a man comes out of the vehicle, asking JJJ to get into the limousine. JJJ irritably accepts and is confronted to Senator Stewart Ward who wishes to discuss the madman-beneath-the-city story.

ACT 3: Elsewhere, Betty and Peter are hot on the trail of the assailant when Peter's spider-sense is suddenly set off. He tries to convince Betty to get out of there but it is too late. He is attacked from behind and he falls to the ground. As he starts to black out, he sees Betty disappear into a nearby manhole.

ACT 4: Westchester County. On an estate just outside a little town called Salem Center, home to a group of genetically enhanced individuals both hated and feared by the outside world...mutants. The mutant known as Marrow is angry that Storm, the current leader of the X-Men will not allow her to go to New York City to investigate the recent disappearances (Marrow used to be a Morlocks and she fears that Callisto, leader of the Morlocks, may be in danger). Marrow angrily tears the Daily Bugle she was holding. Meanwhile, at the hospital, Peter regains consciousness. His wife, Mary Jane, his aunt, May, and Jill Stacy are all there. Peter immediately wants to go back out to look for Betty but MJ reminds him that he is not Spider-Man anymore and that it is someone else's responsibility. At that moment, Flash Thompson storms into the hospital room and immediately lays blame on Peter for Betty's disappearance, claiming that Peter did not lift a finger to help her. He leaves the room fuming just as J. Jonah Jameson walks in. JJJ tells Peter that he is sorry that Betty disappeared and that he wants him to back off of the story. He then walks out, looking suspicious.

ACT 5: A short time later, Peter, dressed as Spider-Man, sneaks out of his apartment, unknown to his aunt May, and Jill Stacy, who is visiting. Miles away, Marrow sneaks out of the X-Men Mansion, unknown to Storm, current leader of the X-men.

ACT 6: Meanwhile, an angry mob of citizens, including Flash Thompson, are threatening to take the law into their own hands by heading into the sewers and finding the culprit behind the recent kidnappings. The police are on the scene but have a very difficult time controlling the crowd...that is, until Marrow shows up and attacks them. Luckily, Spider-Man happens to be in the neighborhood and he momentarily stops Marrow from injuring anybody by webbing her up. Marrow escapes his webbing and heads straight into the sewers; dispersing the crowd at the same time using large barrels. Spider-Man follows her in while Flash Thompson follows him in.

ACT 7: A short time later, in tunnels belonging to the mutant outcasts known as the Morlocks, Marrow picks up the scent of Callisto amidst the nothingness of the empty tunnel. Spider-Man drops in and manages to convince her to join forces with him to bring down whatever is causing the kidnappings. Suddenly, they hear a scream coming from somewhere in the sewers so they both rush towards the source. They discover everybody that had been kidnapped so they start freeing them from the bonds tying them. On cue, the culprit behind the kidnappings arrives. His name is Hunger and he is some kind of super-powered vampire. Seeing that his victims are escaping him, he tries to catch them but Spider-Man and Marrow are there to stop him. However, Hunger is extremely powerful and he grabs both Marrow and Spider-Man by the throat and he starts squeezing the life out of them. Flash Thompson suddenly appears and tries to tackle Hunger, but the latter knocks him out with a mere swipe of his hand. Marrow, who is still being held up by Hunger, screams at Spider-Man, who was released when Flash tried to tackle Hunger, to break one of the bones off of her back and to drive it through the vampire's heart at once. But Spider-Man has vowed never to kill anyone so he refuses to do it. However, he starts pummeling Hunger until the latter starts bleeding. Confused that Spider-Man is not trying to kill him, Hunger stops fighting and disappears. Spidey grabs Flash and Betty and they head back to the surface, leaving Marrow to take care of Callisto and the other Morlocks.

ACT 8: Senator Stewart Ward is revealed to be the powerful figure behind the whole thing.