Intro: Leatherhead voice-over as we open in a nightmare scenario, where we see the mutant gator being tormented by a shadowy creature. As LH is cornered by the beast, we discover that the monster is himself.
Act 1: Open in Turtle lair with Leatherhead and Splinter drinking tea. The Sensei informs the gator that he is welcome to live with them. As the Turtles come in and enthusiastically ask LH to join them for various activities, Leatherhead accidentally breaks the tea cup and pot. As the giant fumbles around and tries to pick up the pieces, Raph nudges him and teases him. The joke does not amuse Leatherhead and he gets extremely angry and violent, pushing Raphael backwards. LH totally loses his cool and runs through a door to escape. The TMNT are shocked by the gator's over reaction, and they pursue their friend to see what's wrong. Raphael apologizes to LH, who in return apologizes to Raph for his rash behavior. Leatherhead explains that he's been having serious problems controlling his temper ever since Bishop performed gruesome experiments on him.
In the sewers we see a man with a large gun accompanied by a waist-high robot. The hunter is named Mr. Marlin, and he's found Leatherhead's tracks in the mud. The robot hands the man a newspaper clipping with a headline regarding a giant croc being seen in the city's sewers. Marlin is pleased that he's found the trail.
Back at the lair, everyone is sleeping. Leatherhead is having nightmares that feature grotesque versions of Bishop, Shredder, Baxter Stockman, and even the Turtles. All of the ghouls are attacking LH - until eventually a monstrous Michelangelo begins to call out to him to wake up. As Leatherhead awakens, the real Mikey is standing over him, looking worried. Leatherhead jumps up in a rage, grabs Mike, slams him into a wall and then onto the floor.
Act 2: As the rest of the Turtles and Splinter run in, Leatherhead (thinking he killed Mike) runs out ashamed and angry with himself. As Mike comes to, the Turtles decide that they had better go find their troubled friend.
Cut to sewers, where Mr. Marlin finds a fresh croc print. His robot side-kick plants a group of sensors that are linked to the hunter's wristband computer.
As the Turtles follow the tracks, the sensors are activated. Marlin picks up infrared pictures of the TMNT on his wristband, so he doubles back to check it out. The hunter discovers the unique prints left by the Turtles and decides to add some extra surprises for his treasured prey.
The TMNT continue following Leatherhead's trail when Raph inadvertently triggers a trip wire. Robotic guns burst from the ground and begin firing lasers at our heroes. The Turtles leap into action and quickly destroy all of the weapons. The TMNT realize that they'll have to be extra cautious. Unfortunately just as they're discussing this, Leo steps on a land mine hidden in the sewer water.
Act 3: Using a shuriken and Don’s bo staff, the Turtles are able to free Leo and take cover as the mines go off in a domino-like effect.
Leatherhead is now in another part of the sewer, traumatized and crying over what he's become. As the not-so-gentle giant sits there and laments his condition, he is met by the sound of Marlin cocking his gun. As the hunter gets ready to fire, Leatherhead openly welcomes his death, stating that he deserves to die because he's nothing but a monster. At the sight and sound of a talking crocodile, Marlin pauses in amazement. Talking to his gun (which he named Betsy), the hunter proclaims that he will be famous for not only bagging a talking croc, but also capturing four giant turtles. With this, Leatherhead’s demeanor changes from docile to violent, as he will not let anyone hurt his friends. LH attacks and grabs Marlin’s gun in his jaws. The man cries out protectively of "Betsy" and then activates an electroshock in the weapon that knocks the mutant unconscious. With the croc incapacitated, Marlin gets an idea to how he can trap the Turtles.
The Turtles discover a passage way blocked with deadly lasers. Leonardo acrobatically leaps through the maze of deadly lights and his brothers soon follow. The guys come across a huge room with a bridge that connects five separate tunnels . Hanging from a catwalk in the middle of the cavern is Leatherhead. As the TMNT move in to rescue their friend, we see Marlin hidden above, and he has Mike in his sights.
Act 4: As the hunter is about to shoot Mike, Leo spots a reflection from the gun and pushes his brother out of the way. Jumping off the catwalk and onto sewer pipes that clutter the space, the Turtles counter-attack Marlin. The hunter fires wildly, missing the Turtles but hitting the ropes that are holding up Leatherhead. The gator plummets into the whirlpool below.
Mike, Don and Raph dive into the water to save the unconscious mutant while Leonardo grapples with the man. Marlin is no match for the ninja, and the hunter is tossed down onto the bridge where he's knocked unconscious (and his gone is broken). Leo dives into the water to assist his brothers, who cannot get free of the the pull of a giant fan at the bottom of the pool. With Leonardo's assistance, Don is now free to attack the fan blades - the crafty Turtle plunges his bo into the blades, which slows down their rotation and eventually stops them (although the staff is half destroyed in the process). The Turtles help LH to safety and Leo cuts the ropes that are binding him. Leatherhead recovers and sees Michelangelo. The gator is ecstatic to discover that he didn't kill his friend.
As our heroes prepare to depart, they discover that Marlin is gone. As the group begins to cross the bridge, Marlin arrives, holding his gun, which is now sparking and about to explode. The hunter explains that the explosion will kill everyone. With that, Leatherhead attacks Marlin. Both fall over the side of the bridge (along with the gun) and crash into the pool below. A massive geyser of water indicates that the weapon has, indeed, exploded with tremendous force.
The Turtles see no sign of their friend. Don observes that Leatherhead gave his life to save theirs - but then the gator pulls himself up from under the bridge to reveal that he did not fall into the pool with Marlin and the gun. Everyone is very happy and they head for the lair. As the group progresses, Leatherhead states that he cannot live with them, as his temper is too much of a threat. The Turtles protest and state that they can help LH learn to live with his condition, but the gator is insistent. Donatello gets an idea...
The Turtles take Leatherhead to an abandoned subway station. The place is elaborately decorated and LH finds it to be beautiful. Don reveals that it's only three minutes from the Turtles' lair, so they'll be nearby if he ever needs their assistance. Leatherhead is overcome with joy and thanks his friends. Mikey states that no thanks are necessary - mutants have to stick together, just like family.