Since the comics appeared back in 1984, there have been two cartoon series, a live-action TV show, 4 movies and two comic book canons. With all these canons around, it's hard to settle on which would be the one definitive world.
Throughout the years, the creators of TMNT have attempted to blur the lines between worlds, and what I'm setting out to do here is settle on the greatest TMNT stories and characters and lining them up in a way that makes one cohesive timeline/canon.
Here is the first part of Merging Canon -- Shredder and his minions.
MERGING CANON (Part 1)
Hun/Tatsu - Shredder's Righthand Man
In merging the canon, Shredder will have not one, bu

In the merged canon, Shredder has Tatsu and Hun to remind Shredder who he really is. When Hun’s thuggish ways blind the Shredder, Tatsu will remind him that he is still a ninja warrior, and vice versa. Instead of just bodyguards, Tatsu and Hun will be more of a council for Shredder. Hun will be Shredder's liasion for the Purple Dragon gang, while Tatsu will oversee the Foot Clan faction.
Krang/Shredder
In the 2003 series, Shredder was actually an evil Utrom-- something that never truly sat well with me. I understand that the creators wanted to associate the Utrom’s crashlanding with the Shredder and the Turtles, but the idea that a body-less Utrom becoming a ninja master in Feudal Japan and raising a young girl as its daughter is about as ludicrous as can get-- and in a show where there are giant turtles doing karate, that says a lot.

In the merged canon, I would have Krang as the evil Utrom who forces the Utrom’s to crashland on Earth, and not in Feudal Japan, but approximately 20 years in the past. There, Krang will meet with Oruku Saki, who both benefit from their partnership and rise quickly to become the Shredder and Krang, from hiding from the Utroms.
Mystic Shredder
In Season 6 of the 2003 series, it was finally revealed that the evil Utrom that would become Shredder, was actually inspired by the lore of a real Oruku Saki/Shredder.
This Shredder only exists in this canon, however, since we are merging canon here, I would like to keep this story, but make this Shredder a forefather of Oruku Saki.
Bebop and Rocksteady/Tokka and Rahzar
Bebop and Rocksteady was Shredder’s idiotic henchmen in the 80’s series. They were gang members of an unnamed gang who unknowingly volunteered to become mutated. What some may not have noticed, Bebop and Rocksteady actually appear in the 2003 series as Purple Dragon members.
Tokka and Rahzar were supposed to be Bebop and Rocksteady’s replacements for the movies canon, but they became so popular, that they later appeared in the 80’s cartoon anyways, but in a different capacity-- they were monsters (of unknown origin) being hunted by a monster hunter.

Tatsu decides to choose a wolf and snapping turtle to become Tokka and Rahzar (pretty much following the TMNT2 plot), while Hun chooses two of his strongest Purple Dragon members to mutate into Bebop and Rocksteady.
Punk Frogs
The poor Punk Frogs only appeared in the 80's cartoon series. Even in that canon, they were poorly used for a one-shot episode and cast away -- Shredder went to Florida, found the mutated frogs and gave them weapons and names and sent them off to fight the Turtles.
The idea that Shredder would attempt to raise his own group of mutant amphibians was pretty badass and I would definitely like to acknowledge it in the merged canon (sans the hillbilly voices, of course).
In the merged canon, however, I want Shredder's attempt to raise and train these frogs to be the highlight of their origin. Maybe Shredder decides that he has been dealt enough defeat by the hands of the Turtles, and concocts a battle plan to create his own team of Punk Frogs to prey on the weaknesses of the Turtles. Shredder goes on a sabbatical (plenty of character development opportunities here) and leaves Tatsu and Hun to watch over things as he goes off to raise his frogs and make them masters of their weapons.
I would make the frogs as disciplined as the Turtles -- especially their leader Atilla. Whether they become allies with the Turtles or not, really doesn't matter to me.
Baxter Stockman/Chaplin
Baxter exists in the comics, and both cartoon series, however, he appears in two different ways. There is the black Baxter which appears in the comics and 2003 cartoon series who eventually turns into a cyborg, and the Igor-ish redhead from the 80's series who eventually turns into a fly.
