After the death of Oroku Saki, The Shredder, several members of the Foot, as well as the Shredder himself seemingly resurrected, would jump and beat Leonardo to the brink of death, and throw his body through the window of the turtles ally April's Second Time Around store. Shredder and the Foot would attack the TMNT, setting the building on fire, and with the help of Casey Jones, they escaped to his grandmother's old farmhouse in Northampton, Massachusetts.
After months of recuperation, the TMNT returned to New York to settle the score with their enemies, and with the help of Zog, a Triceraton mentally confused due to breathing our Earth oxygen, they went to take down the Foot and the Shredder once and for all. During the fight, Zog gets hacked to death by 3 deformed "Mutant Shredder clones". The other Turtles would face them and be taken down one by one, leaving Leonardo to go ahead and face the "real" Shredder himself.
Leonardo faced off against the Shredder alone in which Shredder revealed that he was a worm clone of the original Shredder, but still harbored the hatred of the original. The Foot employed some sort of mystic worms that ate remains of the dead, and then grow into the form of what they ate. The malformed Shredder Elite were the first three experiments with the worms, and the Shredder now facing Leonardo was their fourth. Shredder and Leonardo fought it out and in the end, Leo would end up decapitating him finally killing him. Leonardo would then take Shredder's body and burn it at the Hudson River in a Viking funeral (burning on a raft on a river). With the Shredder gone, chaos erupted in New York Cityamong the leaderless Foot Clan.
Tales of the TMNT
It is shown that after Leonardo defeated the Shredder, he had yet another resurrection of sort, a Foot Mysticnamed Mashima would find the remains and use the mysterious worms that created Shredder's clone body again, which had gained sentience, the worms then went out to find a new body, but this time they'd also eat the remains of a shark. This shark monster retained Saki's memories and considered himself the real Oroku Saki. This creature wasted no time and started his revenge against the Turtles and Splinter kidnapping him. Facing the Turtles, who defeated it, after a long struggle, in which, by the mysterious abilities of this new creature, the personalities of the Turtles were turned upside down, by severing it's connection to the mystic, he realized he was just a clone and escaped, also eating the Foot Mystic.
Sometime later, the monster returned, however, and had the Foot kidnap Casey's adopted daughter Shadow to lure the Turtles into a trap. With the Turtles away this Shark/Worm/Shredder monster would face Splinter and Casey Jones. They defeated this incarnation of Shredder with the help of the Foot Mystic Mashima, who had meanwhile merged with the Shredder Shark clone, and rescued Shadow finally killing the creature.