In TMNT: Adventures issues number forty-two through forty-four (i.e., the issues in which the TMNT, Splinter, and Ninja are brought forward to the future by the future counterparts of Donatello and Raphael) had the TMNT abducted from the past and thus could cause a paradox in that no TMNT in the past, no TMNT in the future. Furthermore, Armaggon mentions how Shredder once possessed the third eye of Sarnath, yet the future counterpart of Donatello claims this particular eye to be the first. Happy holidays!

Archie??

Yeah, Archie licensed the rights to do the Teenage Mutant Ninja Turtles, based on the cartoon show, and they did a number of spin-off comics as well.

This was created before I became mod of Comic Books, so I think I assumed this was a spin-off, although rereading D's comment, I'm wondering if it was just a storyline in the regular book?