Some TMNT stuff really isn't for little kids.
In the Archie's comics series, while drawn in the fashion of the 1987-1996 animated series, the Shredder was shown to be more intelligent, ruthless and competent. The Archie's series used the same background as the 1987 cartoon, as the original three-issue miniseries is identical to the first five episodes. At first he also fought with Krang against the Turtles and tried to take the Turnstone. But when Krang was banished by Cherubea, he fought alone. His schemes were more ingenious, and he was shown to form alliances with other villains (such as Verminator X) while hoping to reap all the rewards himself. His collaboration with Krang finally ended when he came to Earth one last time and tried to take over Shredder's body. Later in the Archie comics, The Shredder travels to the future and works with Armaggon and Verminator X to offset the skill and experience of the future versions of the Ninja Turtles.
It turned out that when he fled from the Turtles after the battle for the first splinter of the Eye of Sarnath, he ran straight into Armaggon, who had landed in the present through a timeslip. Without a way out he fled with him 100 years into the future. From then on they worked together to build their own timeslip generator.
This version of the character was more in line with the early episodes' depiction of the character as a cunning adversary and in many issues nearly proves to be a lethal enemy, coming close to defeating the Turtles on a number of occasions, and even aids Armaggon and Verminator X in the defeat and capture of two of the turtles in the future. But the Turtles defeated the three, and they were washed away by incoming seawater.
His final fate within the Archie comics series remains unknown, though the three-part finale The Year of the Turtle saga, put out by Archie comics after the end of their regular comic series seems to indicate he remains a consistent foe to the Turtles for many years, briefly restoring Splinter to the form of Hamato Yoshi and also undoing Michaelangelo's mutation, though both later revert to mutant status by the end of the story. Shredder was left in a vegetated state in the aftermath of his final battle with the Turtles.