The Shredder appears in 3 episodes of the Saban produced series, Ninja Turtles: The Next Mutation. He is mentioned in a few others. He is once again the head of the Foot Clan and the sworn enemy of the Turtles and their sensei, Master Splinter, whom he desires revenge upon after the rat scarred him many years ago. The Foot of this series appear a lot more clumsy and less intelligent (due to comic relief values), much to their master's irritation. This Shredder is implied to have killed Hamato Yoshi, sliced Splinter's ear, and battled Splinter and the Turtles constantly for many years, as the Turtles are now 18 years old. When Splinter falls ill, Shredder decides to unleash the full fury of his army upon the Turtles' lair, which has recently been discovered by his forces. The sheer numbers of the expanding Foot clan easily overwhelm the Turtles in combat and Shredder then prepares to finish them off, vowing to destroy their leader as well. However, he meets his match at the hands of the recently arrived fifth turtle, Venus de Milo, who using her Shinobi magic, drives the Foot leader insane by calling the true Oroku Saki to the surface to take control, thereby destroying the Shredder, seemingly forever. Afterwards the Foot disbands and Saki begins living on the streets.
When Rank soldiers attack him in order to obtain an ancient ninja amulet in his possession, he is temporarily brought to live with the Turtles by Splinter, far out of the reach of the evil Dragon Lord. Despite the situation, Saki is hate-filled and ungrateful, and the Turtles are none too happy sharing a homestead with their former arch nemesis either. In the episode's conclusion, Saki rejects the Dragon Lord's offer to join forces with him, but is defeated by his new enemy. He manages to escape with the amulet during the ensuing battle between the Dragon Lord and the Turtles. He then appears alone in a deserted alley, where he appears to unlock the amulet's true power, laughing maniacally as he does so.
This greatly implies that Saki would have gone back to his old ways in season 2, likely once again becoming the Shredder, reforming the Foot clan and either declaring war upon or allying himself with the Dragon Lord. However, the Next Mutation was cancelled before this could occur. Another time Shredder was mentioned was when Splinter stated that the Dragon Lord's formidability as an opponent made him miss and long for the malevolence of the Shredder.
- In the Next Mutation, the Shredder has a scar on the right side of his eye.
- Next Mutation is the only incarnation of Shredder that does not wear spike shoulder pad on his armor.