Teenage Mutant Ninja Turtles (2003 TV series) (season 4)

With their bodies bruised and their spirits wounded, the gang returns to the countryside to heal. Unfortunately, their recuperation is interrupted when Casey's cousin, Sid, shows up demanding money, which he needs to repay a debt to the Purple Dragons. Based on Tales of the Teenage Mutant Ninja Turtles #1

The Turtles go on a camping trip in the forest and explore an abandoned sawmill. Their sojourn is interrupted by an extraterrestrial mech that crashes into the nearby lake. The Turtles meet an alien, Jhanna, who is nominated to fight the corrupt Moriah in fair combat. When Moriah arrives on Earth, bringing with her an unfair advantage, the Turtles rush to Jhanna's aid. Meanwhile at the farm, Casey struggles to express his true feelings for April. Based on Teenage Mutant Ninja Turtles #13

Still recovering in the countryside, the Turtles, April and Casey take a raft down the Connecticut River. April confronts Leonardo about his newfound ire and brooding attitude. As Leo expresses his resentment and shame from his last encounter with the Shredder, they are interrupted by a fish-like humanoid creature covered in radiation burns from a nearby nuclear power plant which possesses April's body and tells her of her past. Based on Teenage Mutant Ninja Turtles #28

Hun returns to the Purple Dragons and heads a campaign hijacking weapons shipments. Leonardo's newfound fury leads him to recruit Casey to put a stop to these thefts; however, when the two confront the Purple Dragons after a train hijacking, they encounter a foe that is a danger to all of them.

Villain: Hun

The Turtles and Casey take their training to an abandoned brickworks and practice stealth in a game of hide and seek. Their training is soon interrupted by an enigmatic figure bandaged from head to toe. The man, who seems to have a special relationship with rats, attacks the team viciously and captures Michelangelo. Leonardo rambunctiously retaliates, to the chagrin of his brothers and Casey. Unbeknownst to them, the Turtles have played a large role in this stranger's dark past. Based on Tales of the Teenage Mutant Ninja Turtles #4

Michelangelo is challenged by his former Battle Nexus rival, Kluh, who feels that an interference during their final match gave Mikey an unfair opportunity to win. Given the fluke-like nature of his victory, Mikey turns to Leonardo for help in training him to deal with an opponent twice his size. Despite his claims of unfairness, Kluh's father places a spell on the Battle Nexus to ensure that the rematch is a fight to the death.

During a night-time training exercise on the rooftops of New York City, the Turtles are interrupted by two warring Avians, a race whose appearance resembles angels. The Turtles come to the aid of Raptarr, who is trying to stop the exiled Mephos from starting a civil war in the Avian city and conquering the Earth.

During a meditation session, Master Splinter's sudden collapse is the first of a nightmarish chain of events, which force the Turtles to face death, destruction, and tragedy. Matters become worse as they come face-to-face with their most contentious foes, who, forming an alliance, seek to break the Turtles' spirits.

When the president threatens to cut the funding of the Earth Protection Force, Agent Bishop engineers an alien invasion to attack the president during a press conference before a meeting at the United Nations.

As Hun expands the Purple Dragons' power via illicit arms trades, the Turtles and Casey Jones seek to stop him yet again. Leonardo continues to unduly press his brothers while Casey seeks revenge on Hun for causing a tragic event during his childhood.

Nobody returns and reaches out to the Turtles and asks their help in stopping his foe, Ruffington, and the Purple Dragons from selling weapons to a violent street gang, the Turks.

The Turtles are preparing to celebrate Halloween—one of the few times in the year where they can be seen in public. When costumed thieves steal a statue from April's antique shop, the Turtles put aside their jack-o'-lanterns and pursue them. This theft is part of a bigger plan by a sorcerer, the King of Thieves, who plans to use the statue to unleash a legion of minions on the city. When the Turtles come to disrupt his plans, the sorcerer summons the Thievery God, bringing the statue to life; it then sets out to destroy the Turtles.

Villain: The King of Thieves

Master Splinter invites Miyamoto Usagi—and the irresponsible, sloppy Murakami Gennosuke—from their dimension to Earth in the hopes that Usagi can speak to Leonardo about his wayward attitude. When Gen wanders off to explore downtown Manhattan, the Turtles, Usagi and Casey set out to find him. Their search becomes complicated when an assassin, sent after Leonardo by Lord Hebi, follows Gen and Usagi to Earth.

When Leonardo's anger causes him to injure Splinter, he seeks redemption by travelling to Japan. There, he begins a quest to find the Ancient One, who once trained Splinter's sensei, Hamato Yoshi.

With Leonardo gone, Splinter, Raphael, Donatello and Michelangelo witness the return of the Shredder. They are plunged into the fight of their lives as they ward off volleys of Foot Ninja and Foot Mechs that lay waste to their lair.

Leonardo returns home to find the lair in ruins and his family missing. His search for answers and his family eventually lead him to the realization that Karai is no longer an ally.

Following the invasion engineered by Agent Bishop, genetic material from the replicated aliens combines with inhabitants of the sewers and surrounding waterways, causing a mutant outbreak. Fearing the spread of outbreak, Bishop sends Baxter Stockman to contain the threat. Meanwhile, the Turtles search for items to furnish their new lair, but now must face the threat of attacking mutants.

April discovers a distress signal from her Uncle Augie, who became trapped in another dimension years ago. She appeals to Donatello for help and they use April's puzzle cube to travel across the multiverse. They find Augie, along with his new lizard-like friends, the Brotherhood, who claim they wish to help the inhabitants of Earth. Unfortunately, they soon discover the Brotherhood's true aspirations are not so benevolent.

The mutant outbreak continues to spread throughout the sewers and subway tunnels while the Turtles try to contain the threat. Back at Area 51, Baxter Stockman prepares a new body for cerebral transfer despite warnings from Agent Bishop. When Stockman's body begins to show signs of rejection, he becomes delirious, which leads to a rampage against the person he believes to have caused all his problems, April O'Neil. In the end, seeing April as his mother due to his delusions, Stockman sacrifices himself by being drowned in the East River while handing her to the Turtles and Casey.

Villain: Baxter Stockman

Savanti Romero plots his revenge against the Turtles and Renet after they had him banished to the Cretaceous period. Using his magic to manipulate time, Romero lures the Turtles and Renet into a trap to obtain the time sceptre. Based on Tales of the Teenage Mutant Ninja Turtles #7

Having travelled to the past, the Turtles and Renet battle with Savanti Romero and his telepathically controlled dinosaurs as Savanti attempts to change the historic timeline by preventing the dinosaur extinction event.

When the power goes out in their lair, the Turtles and Splinter gather around the candlelight as Leonardo tells a story he learned from the Ancient One about Splinter's sensei, Hamato Yoshi.

The Turtles continue to deal with the seemingly unstoppable mutant outbreak, but they leave Donatello under care of April and Casey when he becomes very ill. However, Donatello's illness is not just a cold; he is in the final stages of a secondary mutation that will transform him into a savage beast, to which the other turtles and Leatherhead must work together to capture. Meanwhile, Bishop recovers Stockman's brain from the bottom of the East River and resurrects Stockman giving him the half monster, half cyborg body.

When it is apparent that Donatello's secondary mutation is causing his body to degenerate, the Turtles and Leatherhead agree they must go directly to Agent Bishop's headquarters to demand a cure. This scenario proves to be fortuitous as Bishop offers to help the Turtles if they retrieve an ancient piece of technology from the Foot.

The Turtles agree to Bishop's offer in exchange for the cure to Donatello's secondary mutation. They are charged with infiltrating the Foot's headquarters and retrieving the Heart of Tengu. However, Bishop does not have a cure for Donatello and the retrieval of the Heart of Tengu turns out to be the groundwork for a plan that even Bishop doesn't understand.

Still recovering from his secondary mutation, Donatello feels cooped up inside the new lair. To help their brother out, the other Turtles decide to take Don topside to get some much needed air. The Turtles are then ambushed and captured by masked wooden warriors. The Turtles arrive before the Ninja Tribunal, four beings with a great resemblance to the Shredder. Along with four other warriors, the Tribunal entreats the group for aid against a greater evil.