Seasons 1–4

Compared to the predominantly comedic approach of the 1987 TV series, the 2003 series more closely matches the serious tone of the original comics, with a greater emphasis on action and themes of familial bonds. The series adapts a large scope of story arcs from the comics, with the Turtles' adventures combining elements of both fantasy and science fiction.

The first season starts with the Turtles' Lair being destroyed by Mousers, robots made by Baxter Stockman. On the hunt for a new place to live, the Turtles go topside and run into the Purple Dragons, who they later discover is led by Hun. The Turtles eventually get to the source of the Mousers and rescue April O'Neil, who after this becomes the Turtles' most trusted friend. Halfway through the season, Leonardo is approached by the Foot Clan leader Oroku Saki, later learned to be The Shredder, who funded Baxter's Mouser project and is Hun's master. The Shredder attacks the Turtles and burns down April's home, forcing them, April, and Casey Jones to flee the city. When the Turtles return to New York they confront the Shredder once more and Master Splinter goes missing, leading to the introduction of the Utroms, an alien race secretly living on Earth.

Season Two starts with the brothers being sent into space in the middle of a war between two alien races, the Triceraton Republic and the Federation. Upon returning to Earth, the Turtles learn from the Utroms the origins of the Shredder. This season also introduces Karai, Shredder's daughter and pupil, when she comes to take control of New York during a gang war. The season ends in a four-parter with the Turtles and Splinter taking part in the Battle Nexus tournament.

In Season Three, the Triceratons and Federation bring their war to Earth with the Turtles having to help end the war to save their planet. Agent John Bishop, leader of the Earth Protection Force, is introduced as an independent antagonist fighting both the Turtles and the Foot. The Turtles meet Renet, an apprentice timestress, which leads to them being scattered into different worlds/timelines. The Turtles and their allies then confront Shredder for a final battle when he attempts to leave Earth to wage war upon the cosmos.

Season Four sees the Turtles recovering from their final battle with Shredder, particularly Leonardo who suffers from post-traumatic stress disorder. Karai takes leadership of the Foot, Hun leaves to reform the Purple Dragons into a powerful crime syndicate, and Bishop stages a faux alien invasion to secure funding for the EPF. However, lingering consequences from Bishop's engineered invasion caused an outbreak of mutations in New York.

Ninja Tribunal

Season Five introduces the Ninja Tribunal, a council of ninjitsu demigods who conscript the Turtles as acolytes to protect the world from the original Shredder, a dark evil coming back into being who threatens to set the world into darkness. During this season, the Turtles go through many trials and tribulations on their journey to become the best fighters they can be, eventually tapping into ancient energy to defeat the original Shredder. This would be the last to use the original character designs and animation style with its plot concluding the series' main storyline.

Fast Forward

The sixth season, subtitled "Fast Forward", would retool the series with a new art style and comedic tone. The season's plot focuses on the Turtles being transported about 100 years into the future to the year 2105; where they meet and befriend Cody Jones, the great-grandson of April and Casey. They must also contend with futurist enemies like Sh'Okanabo and his minion Viral as well as dealing with the activities of Cody's greedy and ambitious uncle Darius Dunn.

Back to the Sewer

The series would conclude in the seventh and final season, titled "TMNT: Back to the Sewer", while sporting another redesign for the entire cast based on the designs from the 2007 TMNT film. After returning to the present day, the Turtles must battle a cybernetic version of the Shredder which was the result of Viral merging with the data of the exiled Utrom Shredder. There is also a running subplot centered on the engagement and wedding of April and Casey.

Turtles Forever

The 2009 television film serves as the actual four-part finale to the 2003 series and centers around the Turtles encountering their 1987 animated counterparts, who have accidentally been transported to the 2003 Ninja Turtles' reality. To make matters worse, the 80's Shredder and Krang as well as their minions Bebop and Rocksteady free Ch'rell from his imprisonment as the redesigned Hun and Karai realign themselves with the released Ch'rell.

Main

• Leonardo (voiced by Michael Sinterniklaas) is the oldest brother and the leader of the team who wields two Katana.
• Donatello (voiced by Sam Riegel) is the second youngest brother and the brains of the team who is in charge of creating their gadgets, he wields a bo staff as his weapon.
• Raphael (voiced by Greg Abbey) is the second oldest brother and the muscle of the team who has a temper and sometimes argues with Leo over the actions they must take. He wields two Sais as weapons.
• Michelangelo (voiced by Wayne Grayson) is the youngest brother and the jokester of the team. He loves comic books and sometimes disguises himself as the superhero Turtle Titan. His weapon of choice is Nunchucks.
• Splinter (voiced by Darren Dunstan) is the master and father of the Turtles who finds them prior to their mutation and trains them in Ninjutsu. Prior to his mutation, he was the pet of Hamato Yoshi and learned ninjutsu by mimicking his moves.

Allies

• April O'Neil (voiced by Veronica Taylor) is a human who used to be Dr. Stockman's assistant, but after learning his ulterior motives is saved by the Turtles and becomes their friend.
• Casey Jones (voiced by Marc Thompson) is a human whose father's shop was set on fire by the Purple Dragon and they later killed his father. He became a vigilante to fight them but has anger issues, but manages to tune it down after meeting and befriending the Turtles.
• Mortu (voiced by Dan Green) is a benevolent Utrom and an ally of the Turtles. He was the captain of the ship which was transporting the imprisoned Ch'rell on board and became stranded on Earth with his fellow Utroms when Ch'rell escaped and caused them to crash. He later met Hamato Yoshi and recruited him to become a guardian of the Utroms. He later saved the Turtles from their final battle with the Utrom Shredder and had him stand trial for his crimes.
• Ninja Tribunal is a group of four ninja masters. They were once five warriors who defeated the Tengu Shredder, but one of them, Oroku Saki, made a deal with the demon and allowed his spirit to inhabit his body in exchange for power. The other four traveled across the world and trained their body and spirit to counter their old comrade and ultimately succeed in sealing him away. Afterwards, they tried to prevent his return and passed their knowledge of martial arts, which later came to be known as Ninjutsu to others.
  • Kon Shisho (voiced by David Zen Mansley) is a member of the Ninja Tribunal and the master of spirit.
  • Juto Shisho (voiced by Marc Thompson) is a member of the Ninja Tribunal and the master of weapons.
  • Chikara Shisho (voiced by Lenore Zann) is a member of the Ninja Tribunal with bandaged feet and legs who is the master of strength.
  • Hisomi Shisho is a member of the Ninja Tribunal. As the largest of the group, he is the master of stealth who is always silent.
• The Ancient One (voiced by David Chen) is a student of the Ninja Tribunal and the master and father figure of Hamato Yoshi who joins them on their request.
• The Acolytes are the students of the Ninja Tribunal that they seek to train and prepare them for the threat of the Tengu Shredder. They are the Ninja Turtles and four other humans.
  • Faraji Nagala (voiced by David Moo) is an Acolyte who bonds with Leonardo.
  • Adam McKay (voiced by Britton Herring) is an Acolyte who bonds with Donatello.
  • Joei Reynard (voiced by Rebecca Soler) is an Acolyte who bonds with Raphael.
  • Tora Yoshida (voiced by David Chen) is an Acolyte who bonds with Michelangelo.
• Cody Jones (voiced by Christopher C. Adams) is the great-grandson of April and Casey and the heir of the O'Neil Tech. He is the Turtles' friend and guide in the year 2105 during the Fast Forward season. After his Time Portal accidentally brings the Turtles to his time, he helps them to become accustomed to the Earth's new way of life while trying to rebuild the Time Window and send them home.
• Serling (voiced by Marc Thompson) is Cody's loyal robot servant who is usually annoyed by the Turtles, he later gains a battle mode known as Turtle X which Cody can control. When the Turtles are finally going back to their own time, he is infected by Viral and goes with them and later helps the Turtles defeat the Cyber Shredder.

Antagonists

• The Foot Clan is a criminal organization of ninjas dating back to the ancient Japan.
  • Oroku Saki/The Shredder (voiced by Scottie Ray) is the archenemy of the Turtles and Splinter and serves as the main antagonist of the series. Several individuals have used the mantle of Shredder. In a possible future, the Utrom Shredder, Tengu Shredder, and Cyber Shredder are engaged in a war for control of New York City.
    • Ch'rell is a Utrom warlord who masquerades as a benevolent Japanese philanthropist. He has been stranded on earth for centuries and indirectly had a hand in the Turtles and Splinter's creation.
    • The Tengu Shredder from ancient Japan was the original Shredder who was also known as Oroku Saki.
    • The Cyber Shredder is an artificial intelligence copy of Ch'rell that merged with Viral.
  • Karai (voiced by Karen Neill) is Utrom Shredder's adopted daughter and his second in command from the end of season 2, replacing Hun. Due to her sense of honor, she is usually conflicted with orders she receives from the Shredder. After his defeat, she takes control of the Foot and becomes the next Shredder, seeking revenge on the Turtles for her father's exile. After being forced to team up with the Turtles against the Tengu Shredder, she disbands the Foot and declares a truce with them.
  • The Foot Mystics, also known as the Heralds of the Shredder, are five mystic beings, each presenting one of the five elements. They are the servants of the Tengu Shredder and have also served Utrom Shredder and Karai through an artifact known as the Heart of Tengu. After they manipulated the Turtles and Agent Bishop to steal and destroy it, they were freed and set out to revive their master.
    • The Metal Foot Mystic (voiced by Sean Schemmel) is the leader of the Foot Mystics who possesses ferrokinesis.
    • The Earth Foot Mystic (voiced by Sean Schemmel) is a Foot Mystic who possesses geokinesis.
    • The Fire Foot Mystic (voiced by Sean Schemmel) is a Foot Mystic who possesses pyrokinesis.
    • The Water Foot Mystic (voiced by Brian Maillard) is a Foot Mystic who possesses aquakinesis.
    • The Wind Foot Mystic (voiced by Brian Maillard) is a Foot Mystic who possesses aerokinesis.
  • Master Khan (voiced by Sean Schemmel) is a high-ranking Foot Ninja and the first lieutenant of the Cyber Shredder who was rebuilding the Foot Clan for whenever he would return. It was revealed in an alternative future that he had destroyed the Turtles.
  • The Foot Ninjas are the common foot soldiers of the Foot Clan.
• The Purple Dragons are a street gang that is associated with Foot Clan.
  • Hun (voiced by Greg Carey) is the leader of the Purple Dragon and Shredder's second in command until the end of season 2. he was responsible for burning down the shop of Casey's father, as such became his archenemy, he was also going to kill Hamato Yoshi but Splinter left a scar on his face. Hun is very loyal to the Shredder and will do anything to gain his favor. After Ch'rell's defeat, Hun returns to the Purple Dragon and turns it from a street gang into a crime syndicate.
• Baxter Stockman (voiced by Scott Williams) is a scientist working for the Foot clan and the Shredder. After suffering severe punishments at the hands of the Shredder, he starts to scheme against him and after his defeat, joins the Earth Protection Force and Agent Bishop.
• Agent John Bishop (voiced by David Zen Mansley) is the leader of the Earth Protection Force (E.P.F). He was abducted and experimented on by aliens back in 1815 as such he deems any extraterrestrial as a threat, becoming a deadly adversary of the Turtles. After being saved by an alien during a failed experiment, he starts to have second thoughts about them and decides to seek allies instead of enemies which leads to him ultimately becoming President of the Pan Galactic Alliance (P.G.A) and an ally of the Turtles in the Fast Forward season.
• Darius Dun (voiced by David Zen Mansley) is Cody's uncle and guardian and one of the main antagonists of the Fast Forward season. He has taken control of O'Neil Tech and uses it as a cover for his criminal activities which include making weapons and selling them in the black market. He first has a race of endangered warriors known as Inuwashi Gunjin as his slaves and after losing them are provided with the dark counterparts of the Turtles known as Dark Turtles.
• Sh'Okanabo (voiced by Sean Schemmel) is an alien Kanabo warlord and one of the main antagonists of the Fast Forward season. He seeks to unleash the Day of Awakening on Earth, which is turning the inhabitants of Earth into Kanabo Drones, and have his race thrive on Earth until its resources are finished but finds the Earth's sun as an obstacle. To fulfill his plans, he teams up with Darius Dun and gives him the Dark Turtles, monsters that he created by combining the Turtles' DNA with that of Kanabo DNA, and in return receives the blueprints of the Time Window.
  • Viral (voiced by Eva Kaminsky) is a sentient computer virus and Sh'Okanabo's assistant. She aids her master on his quest to bring the Day of Awakening but is ultimately torn to bits by Cody and Serling. Viral returns and uses Serling to get revenge on the Turtles as she goes to their time. Viral accidentally releases the Cyber Shredder from his data storage and becomes a part of him.
• The Dark Turtles are deformed clones of the Ninja Turtles who were created by Sh'Okanabo and controlled by Darius Dun. They were created by combining the DNA of the Ninja Turtles and the DNA of a Kanabo.
  • Dark Leonardo (voiced by Michael Sinterniklaas) is a blue-skinned clone of Leonardo who leads the Dark Turtles and eventually gains a mindset similar to original Leo.
  • Dark Donatello (voiced by Sam Riegel) is a purple-skinned clone of Donatello with wrist guards and a long tail who is the Dark Turtle's residential mad scientist.
  • Dark Raphael (voiced by Greg Abbey) is a red-skinned clone of Raphael with twin talon knuckle dusters who is the most aggressive of the group.
  • Dark Michelangelo (voiced by Wayne Grayson) is a yellow-skinned clone of Michelangelo with orange eyes and a long tongue.

Others

• Hamato Yoshi (voiced by Eric Stuart) is Splinter's owner and a guardian of the Utroms. he was once a homeless boy along with his friend Yukio Mashimi, but both were adopted and trained by the Ancient One and became guardians of the Utroms after learning their secrets. He and Mashimi were in love with Ancient One's daughter Tang Shen who was in love with Yoshi, causing Mashimi to become jealous, murder her, and join the Foot. Yoshi avenges Tang Shen and kills Mashimi for his betrayal. He later moves to New York along with the Utroms, where he's captured and tortured by the Foot Ninjas to reveal the Utrom's location and was murdered by the Shredder when he wouldn't talk. Afterwards, Splinter leaves and eventually finds the Turtles.
• Starlee Hambrath (voiced by Amanda Brown) is a bright and highly intelligent O'Neil Tech intern from the planet Omatran and a friend of Cody and the Turtles in the Fast Forward season. She is shown to have a crush on Cody.
• Torbin Zixx (voiced by David Elliott) is an intergalactic smuggler and mercenary who usually outsmarts the Turtles and uses them for his own end either as an ally or an enemy.