Just spit balling, but there have been at least two female mutant turtle characters in the Turtles series. Venus De Milo and Jennika. Venus was from the series Next Mutation, where she was actually with the brothers, but was left behind by Splinter. Somehow making her way to Chinatown, she was discovered by a shinobi magician called Chung I. Chung I took the turtle with him to China where he raised her as a daughter and named her Mei Pieh Chi. He also trained the turtle in the art of Shinobi.

Jennika or Jenny is part of the comic-verse where she was the ninja chūnin of Splinter's Foot Clan, a dear friend to the Turtles and for a time was a love interest to Casey Jones. Originally human, she is now a mutant turtle after her life was saved by an emergency transfusion of mutagenic blood donated by Leonardo.

But my question is how would you incorporate them into the new series? Would both be regular turtles turned mutant, or would you make Jennika human before becoming a mutant turtle similar to how her comic self was mutated? Just thought I'd ask since so many wonder about them.

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That's a head scratcher.

I don't know about Jennika, but if you incorporate Venus, I'd say have her as a cousin rather then a sister to the turtles, she was from the same shop but was purchased by Chung I a few hours after Yoshi got his turtles, Chung I on his way home found the mutegen that made Splinter and our turtles and was able to use a random jar to scoop some up without touching it, but some time later the jar fell and broke and Venus would be covered in it and mutated (similar to how Latherhead 2003 came to be)

Just like what jisow777 said, I don’t know about Jennika, but If you incorporate Venus, I would like to see Venus as a cousin rather than a sister. It’s ashamed that Jennika cannot be together with Casey Jones in the comics now that she is a mutant turtle.

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I would have them be normal turtles like the brothers.
As for how to incorporate them, I would basically have their origin be the same as the brothers, with a few twists. Venus and Jennika are two different turtles who were adopted by Chung I of the Hamato clan. On his way home, he discovers a canister of mutagen. Chung I picks it up, wondering what it is, and takes it home with the turtle girls. But along the way, he trips and drops both the canister and the turtles. While Chung is lucky enough to escape being mutated, the 2 turtles are covered in mutagen, turning them into mutant turtles just like the brothers. Despite having no idea why this happened, Chung takes the turtle girls home. He eventually decides to raise them as his daughters, and names them Venus De Milo and Jennika. When they are old enough, he begins teaching them the art of Ninjitsu. They remain in hiding for 15 years, but unlike Splinter and the brothers, go undetected by Shredder and the Foot clan. Then at some point, Chung I and his adopted daughters learn of the existence of the 4 brothers in New York. They travel there, meet up with them and the Rainbooms, and become friends.

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So I think you should totally add them in.
It would make the series even more exciting

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Wildcard. You gotta see what I did at Canon and and non-canon forum.

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Raphael needs to go to a mental asylum. He's crazy.

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Wasn’t 2012 Venus just a picture Raphael drew in one of the trucks but okay

Well In IDW Venus Was a human who became one of the mutant punk frogs

Then became forcefully experimented on by a mad scientist and now looks like a patchwork turtle

But what if she was a homunculus

A second creation of victor Frankenstein to fill the void of his lost creation frank from the 2012 monster saga?

As an homage to bride of Frankenstein

My oc could be involved to translate Venus who speaks a foreign language and her bodyguard because of sensitive nature

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Hmm... That's a bit of a toughie.