The Turtles slowly come into conflict with the Foot Clan. After their lair is destroyed by Baxter Stockman's mousers, they find a new home elsewhere in the sewers and also gain new allies in the form of April O'Neil and Casey Jones. The Turtles foil the plans of the Shredder, Hun, and Stockman on numerous occasions before Shredder offers Leonardo a peace offering in exchange for their service, citing an unknown evil they must face together. Splinter reveals the Shredder and Hun's hand in murdering his master Hamato Yoshi, and the two sides come to blows in a battle that seemingly ends in the Shredder's defeat. However, unknown to the Turtles, the Shredder survives, and after his ninjas savagely ambush and wound Leonardo, destroys April's home and believes them dead, though the Turtles, Splinter, Casey and April survive and depart for Casey's family's farm house in rural New York. After Leonardo's wounds heal and their resolve is restored, the group returns to New York to face the Foot Clan. However, after their triumph against the Shredder, Splinter vanishes, and after following a lead from a mysterious group known as the "Guardians", the Turtles discover the Utroms, an alien race hiding amongst humanity, and are unable to save Splinter from them before being teleported into space.

Season 1 Episode 7 - The Way of Invisibility

After Casey Jones makes himself an unwanted guest in the Turtles' lair, Raphael takes him topside for a "breath of fresh air", where they encounter the Foot Tech Ninjas. Air Date : 22nd-Mar-2003

Season 1 Episode 1 - Things Change

In their underground lair deep beneath the city streets, the Turtles and Master Splinter are suddenly attacked by a horde of Mouser robots! Air Date : 8th-Feb-2003  Read More

Season 1 Episode 2 - A Better Mousetrap

The Turtles discover the source of the Mouser robots that trashed their old lair: Dr. Baxter Stockman -- a noted technological genius/inventor, who tries to pass off the Mousers as a means to eradicate the city's rat problem. Air Date : 15th-Feb-2003  Read More

Season 1 Episode 3 - Attack of the Mousers

When April O'Neil wakes up in the Turtle's lair she has major trouble dealing with the reality of four giant talking Turtles and a Zen-master rat. She soon learns of the origin of the Teenage Mutant Ninja Turtles and they realize their common enemy is Baxter Stockman and his army of robotic Mousers. Air Date : 22nd-Feb-2003  Read More

Season 1 Episode 4 - Meet Casey Jones

Raphael is a little cooped up underground with only his brothers and Master Splinter. When Raphael almost clobbers Michelangelo in some brotherly sparring, it's apparent that Raphael needs to get out ... let off a little steam. But when he meets up with Casey Jones, a vigilante erring a little to the right of justice, Raphael must face the reality of his own hothead ways... Air Date : 1st-Mar-2003  Read More

Season 1 Episode 5 - Nano

When a scientist accidentally unleashes a super-powered Nanotech monster with a childlike mind, it adopts a small-time thief as its father figure, and the mayhem begins! Air Date : 8th-Mar-2003  Read More

Season 1 Episode 6 - Darkness on the Edge of Town

The Turtles, investigating a strange blackout, discover the Foot Ninja stealing a Japanese ceremonial sword from the Metropolitan Museum of Art. Air Date : 15th-Mar-2003  Read More

Season 1 Episode 7 - The Way of Invisibility

After Casey Jones makes himself an unwanted guest in the Turtles' lair, Raphael takes him topside for a "breath of fresh air", where they encounter the Foot Tech Ninjas. Air Date : 22nd-Mar-2003  Read More

Season 1 Episode 8 - Fallen Angel

On a nightly training run, the Turtles and Casey Jones break up a Purple Dragon robbery. One of the perps is Angel, a girl Casey knows from the neighborhood who's going through her initiation rites to become a Purple Dragon. Air Date : 29th-Mar-2003  Read More

Season 1 Episode 9 - Garbageman

The boys have made friends with a group of homeless, and are worried when they start mysteriously disappearing into the night! Air Date : 5th-Apr-2003  Read More

Season 1 Episode 10 - The Shredder Strikes (1)

Oroku Saki (aka the Shredder) attempts to convince Leonardo that Saki is fighting the good fight ... that he's out there carrying on the great tradition of Bushido and Ninjitsu, and the turtles should stand with him. Air Date : 12th-Apr-2003  Read More

Season 1 Episode 11 - The Shredder Strikes (2)

Our four turtles stand facing their most formidable foe to date ... the Shredder. Beaten and battle weary, the turtles get separated from one another during the martial arts mayhem and a building collapse! Air Date : 19th-Apr-2003  Read More

Season 1 Episode 12 - The Unconvincing Turtle Titan

Believing the Turtles can accomplish so much more for the city, and inspired by iconic superhero Silver Sentry, Michelangelo decides to take a crack at being a superhero. Air Date : 2nd-May-2003  Read More

Season 1 Episode 13 - Notes from the Underground (1)

When Don's examination of some mysterious crystals attracts the attention of a subterranean monster, the Turtles underground exploration unearths a Foot Genetics Lab! Air Date : 10th-May-2003  Read More

Season 1 Episode 14 - Notes from the Underground (2)

After discovering an abandoned underground Foot Genetics Lab, and being attacked by once-human Digging Creatures, the Turtles assist those very creatures in trying to repair a Force Field. Air Date : 17th-May-2003  Read More

Season 1 Episode 15 - Notes from the Underground (3)

After befriending the once-human creatures in an abandoned underground Foot Genetics Lab, the Turtles join them on a journey deeper into the earth, where they come upon the ruins of a once-great subterranean city. Air Date : 24th-May-2003  Read More

Season 1 Episode 16 - The King

With all the turtles living in April's apartment, things are getting a little crazy. But, when Donatello stumbles upon a fantastic monster in the basement, things get crazier. Air Date : 31st-May-2003  Read More

Season 1 Episode 17 - The Shredder Strikes Back (1)

On a training run Leo is ambushed by a major Foot attack force, including Foot Tech Ninjas, their old enemy Hun, and a new threat: the Foot Elite! Air Date : 7th-Jun-2003  Read More

Season 1 Episode 18 - The Shredder Strikes Back (2)

When the Foot Ninja attack April's apartment in force, the Turtles fight against overwhelming odds to get the wounded Leo to safety. Air Date : 14th-Jun-2003  Read More

Season 1 Episode 19 - Tales of Leo

The Turtles, Splinter, Casey and April just barely manage to escape from the explosion that destroys the antique store. They hit the road and hide out at Casey's grandmother's old farmhouse, but Leonardo is badly wounded. Air Date : 13th-Sep-2003  Read More

Season 1 Episode 20 - The Monster Hunter

Still recuperating up at Casey's grandmother's farm, the turtles are feeling the sting of boredom. Luckily, a scientist known as the "Monster Hunter" has come to the area searching for a legendary monster... Air Date : 20th-Sep-2003  Read More

Season 1 Episode 21 - Return to New York (1)

The Turtles return to New York with one goal in mind: to destroy the Shredder once and for all. Air Date : 27th-Sep-2003  Read More

Season 1 Episode 22 - Return to New York (2)

The Turtles and Splinter continue to fight their way up through the Foot Headquarters skyscraper, facing down three misshapen Mutant Shredder Clones, a hallway of traps, and the Mystic Ninja. Air Date : 4th-Oct-2003  Read More

Season 1 Episode 23 - Return to New York (3)

With Stockman showing up in the middle of the final battle between our heroes and the Shredder, everything is thrown into chaos ... so much so that our heroes must join forces with the Shredder and Hun to defeat Stockman. Air Date : 11th-Oct-2003  Read More

Season 1 Episode 24 - Lone Raph and Cub

With Splinter mysteriously vanished, the Turtles are feeling frustrated, not knowing where to start looking. Impatient with strategizing, Raph heads off on his own - and straight into trouble, of the mobster kind! Air Date : 18th-Oct-2003  Read More

Season 1 Episode 25 - Search for Splinter (1)

After the frustrated Turtles exhaust their search for Splinter, their suspicions turn to the Guardians, and the trail soon leads them to a non-descript building, the initials of its company name spelling out "TCRI." Air Date : 25th-Oct-2003  Read More

Season 1 Episode 26 - Search for Splinter (2)

The Turtles successfully infiltrate the mysterious TCRI Building, where they manage to sneak into its inner sanctum, and locate the unconscious Splinter inside a stasis tank. Air Date : 1st-Nov-2003  Read More