Intro: Leo discusses the ramifications of facing your worst fears as the show opens with a giant, shadowy mass moving through rocky tunnels. As the tentacled beast reaches a cavern, we see Leo defending a weakened Master Splinter, whose eyes flutter shut.
Act 1: Open with the Turtles working on the Battle Shell as Angel beats on the warehouse door frantically. The ninjas open the door and the frightened girl enters. She informs the TMNT that her brother has been missing for three days. The Turtles agree to help their young friend find her brother and the group piles into the Battle Shell. Angel explains that the police are too busy cleaning up the city after the Triceraton invasion to spend time looking for her sibling, and then she shows the Gang Green a gold coin that her brother had found in old building on Wall Street. Angel states that she warned him not to go back there seeking more treasure because she sensed great peril, but the headstrong youth ignored her and left - and he hasn't been seen since.
The Battle Shell soon arrives outside the Volpehart Building, which is unusual and creepy. The Turtles and Angel go inside the structure to investigate. Mikey finds an old bust dated 1616 and Angel hears a nefarious voice in her head that no one else can detect. The girl walks in a half-trance to a wall and lifts a curtain, revealing a symbol-laden control panel. Angel presses the panel and it opens a hidden staircase that leads down. Our heroes descend the stairs and find an ancient sewer tunnel, filled with bones. The tunnel ends at a huge, circular door that has the words "Abandon All Hope Ye Who Enter Here" written in Italian above it. As Angel pushes the door, a symbol on the door glows red, illuminating the sewer. The weird light animates the skeletal remains strewn about the tunnel and they advance on our heroes.
Act 2: As the Turtles fight the skeletons, an old man appears on the staircase and bids them to follow him. The group retreats back up the staircase to the lobby of the Volpehart building - barely reaching ground level ahead of their skeletal attackers.
The old man explains that he is the heir of the man who built this building, C. F. Volpehart (who is featured in the artwork, including the bust that Mikey was investigating). The man tells the Turtles to forget the treasure and go home. Angel explains that they aren't here for the treasure, they're trying to find her brother, Robbie. Volpehart states that he did see the youth and warned him not to hunt for the gold, but the young man ignored him. The old fellow then tells him his story.
Hundreds of years ago, an evil creature crashed to Earth on a meteor. Landing in Manhattan, the monster lured people to it with promises of treasure and then fed off their greed and fear. Eventually the Native Americans knew that the alien had to be destroyed, so one brave fashioned a spearhead from the very meteorite that brought the monster to Earth. Before he could use his weapon, the warrior was slain when the creature's call was heard by a European named C. F. Volpehart. Volpehart had come in search of treasure and killed the brave before he could begin his mission. Volpehart acquired the spear made out of the meteor rock and through the strength of the evil creature, became rich and powerful. The entire island eventually became a world-wide economic center due to the alien's nefarious influence.
The old man explains that he attempted to kill the creature himself with the spear, but it's mental powers were too much for him and he failed. The Turtles take the old man's warnings seriously, but they also know that they're Robbie's only hope. Volpehart gives Leonardo the spear and our heroes head off to face the ancient menace. The TMNT are able to get passed the skeletons thanks to the spear, which also opens the circular doorway. The Turtles enter a gigantic cavern lit by a shard of burning meteor and are surrounded by stone cells that are filled with old corpses. As the ninjas investigate the cells, huge tentacles burst out of the tunnels and begin to attack!
Act 3: The tentacles prove to be a formidable threat, and all four Turtles are quickly captured.
Mikey awakes in a tunnel and spots Leonardo. Leo explains that he's joined the creature. As he emerges from the gloom, we see that Leonardo's left arm is missing and has been replaced with tentacles! Laughing maniacally, Leo attacks his bewildered brother!
Leo awakens covered in muck inside one of the cells. A shadowy figure cuts through the membrane covering the hole and Splinter appears. The Sensei pulls Leonardo out of his prison, but as they walk, the tentacles attack yet again.
Donatello awakens in a tunnel and spots Angel, who laughs and runs away. The brainy Turtle follows and tells her this is no time for games. Angel runs back to the cavern and walks on the ledge by the burning meteor. Don calls out to her to stop it, just as the girl falls into the pit.
Raph opens his eyes and finds himself facing off with the Shredder. As they battle, the villain's helmet and mask fall off, revealing the Shredder to actually be Raphael!
Splinter is captured by the tentacles, lifted high above the ground and squeezed. The beast drops the lifeless body to the ground as Leo rushes to his Master's side, screaming in dread.
Act 4: Leonardo awakens in his cell. Again Splinter pulls Leo out, but this time, after they are free, Splinter's eyes glow red and he attacks his son. As Splinter launches his assault, Leonardo defends himself. The Turtle realizes that these events can't be real, which enrages Splinter - who makes a mad leap at his student. The rat lands on Leonardo and is impaled on the Turtles' katana!
Leo wakes up inside his cell yet again. This time he cuts himself free and then finds Mikey's prison and pulls him out. The ninjas find and free Raph and Don. Leonardo points out that recently occupied cells glow red. Our heroes scan the cavern and quickly spot a glowing cell. Raphael cuts it open and they find Robbie inside. The Turtles pull the youth out, and as he awakens he becomes frightened. Raph explains that they're just figments of his imagination, which seems to calm down Robbie. As the group attempts to retreat, the tentacles attack yet again.
As the Turtles fight the tentacles, Leo finds the meteor spear he had dropped in the initial battle. As the skirmish continues, the entire hideous creature crashes through the floor! The beast tries to use its mind control trick on Leonardo, but the Turtle is ready for the ploy and overcomes it. Leo then throws the spear into the creature’s eye and it disappears in a flash of light.
Cut to the Volpehart Library. As Angel and the old man wait, the fellow begins to sweat profusely and tells the girl that her friends have been successful in defeating the creature. The old timer reveals himself to actually be the original C. F. Volpehart and announces that he is finally free of the creature's influence. The man then begins to fall, and as he drops, his body turns into ash.
The Turtles enter with Robbie in tow. Angel rushes over and hugs her brother as Mikey asks what happened to the old man. The girl informs the ninja that he's standing in what's left of him and Mikey leaps off the pile of ashes, screaming. Our heroes decide that they've had enough weirdness for one night and drive off in the Battle Shell.
Back on the streets, we see a stockbroker near a phone booth that's ringing. As the business man answers the phone, we hear the creature's infernal voice on the other end - promising the man great power and wealth. With that, the broker’s eyes begin to glow red...