Michelangelo, or Mikey as his brothers called him, somehow felt that he was different from his brothers. 

Leo; the obedient teacher's pet of the four, he always placed honor and family above anything else. Though he automatically called himself the oldest as Splinter always did.

Raph; the second oldest and a bit of a hothead, but underneath all that muscle was a guy that would do anything to protect the family no matter what he said.

Donnie; the tech genius of the group, there seemed to be nothing that he couldn't hack into techwise as he sharpened his skill. He wasn't bad with a bo either. 

Then there was Mikey himself. Well, except for one thing...

Mikey was never a HE.

It's best to explain from the beginning. To be honest, even Splinter didn't know at first either.

Back when the turtles were still fairly young children, Mikey seemed to be a little odd. He always stuck to Splinter's side, asking him to help clean up with him before they started to train in ninjutsu. Splinter also recalled that Michelangelo was kept separate from the other turtles in the lab for some reason, which may be a result what Mikey stayed away from his other sons out of instinct or something. 

Mikey also seemed to act differently from his brothers. As they would get into arguments and tussle with each other, Mikey stayed out of the way and sometimes try to stop Raph and Leo's quarrels only to result in getting Splinter to help. 

Mikey also seemed to like stuffed animals, and even liked to draw things that would seem 'girly' and liked to read romantic books, resulting in Raph teasing him about it. But the youngest turtle still liked to skateboard, loved pizza, and practice ninjutsu like the others. 

Things would take a new turn for Mikey shortly after the young turtle turned 8. 

Mikey was currently freaked out when something unusual happened. 

For a few weeks, Mikey had stomach problems and didn't want to be near his brothers. Then came the day he was really panicking.

He actually laid an egg.

He quickly went to Splinter while all his brothers were busy in the sewer.

After showing Splinter the egg, the rat began to realize the reason why Mikey was kept separate from his brothers in the lab.

Mikey was really a she.

Splinter then asked his new-found daughter if she had intercourse with her brothers. Seeing her confused face, he gently explained it to her, and Mikey shook her head and said 'no'. Her egg was a dud. 

After looking over a pet care book concerning turtles, Splinter realized that his only daughter was fertile and her eggs could be fertilized. But seeing as she was a mutant, this would be different, and she could do this once a year. 

Mikey was afraid. She thought that this would mean that Splinter wouldn't let her train with her brothers or learn to be a ninja anymore. Seeing her discomfort, Splinter reassured his daughter he would do nothing of the kind. Mikey also asked her dad if he could still call her 'son' because she didn't want to be treated differently until her brothers found out of their own.

When Splinter asked her why, she simply smiled and said; 'Oh, maybe when the time comes I think we can both imagine the look on their faces when they learn they do have a baby sister and never noticed.' Splinter had to conceal a chuckle at that. Mikey was still her playful self.

"Well, since we've discovered this, I'll be helping you during your season with the eggs from now on till your brothers learn the truth. But, you do know you will have to tell them if any of them find out." Splinter reminded his daughter.

"Sure dad." Mikey smiled.

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After 10 years, Mikey was able to hide her secret well, although there were some complications along the way. 

For one, even though she was a reptile, she gained...breasts. And curves. She had to bind them tightly so he brothers wouldn't know a thing. Mikey also took to wearing shirts whereas her brothers wouldn't. It wasn't much a problem since her shell was so much smaller than theirs.

During that time, Mikey had always had Splinter to help her with the eggs to dispose of them, she never had any young, but it was getting harder when the boys finally hit their season at 16. Raph would be a little pushy, ok maybe really pushy, Leo would act weird, and Donnie would be really twitchy, unable to focus on his tasks. During their heat, Mikey would head off to an abandoned warehouse where she would spend her season in solitude. 

After meeting or reuniting with April, stopping Shredder and Sacks, then the Krang incident, Mikey felt more old than she thought. 

But that won't be the most of her worries.

Because secrets always have a way of coming out.

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Donnie would be proud to say so himself that he was a turtle whose smarts could be worthy of a Nobel Prize, as Mikey once told him.

But right now, he was stumped. 

Mikey was being strange. For a while, maybe longer than he noticed, Mikey had kept a certain distance from his brothers since they were all 8 during the early spring. He wondered if something was wrong with his younger brother. Especially when he and his brothers were in heat. 

Splinter told them since they still retained their primal instincts, they would experience this still. But it would still be a lost cause because there were no other female mutants that they knew of, so they were endangered either way. 

Right now, he was looking over something in the new med center for the lair. He was looking up the blood samples from his siblings when he finally got to Mikey's. But he began to find something.

Puzzled, he checked again. And Again. AND AGAIN.

If Donnie's eyes couldn't get any bigger behind his glasses, he was wrong. They could've been the size of dinner plates.

"How did...Did he...no she, ugh! How could I have been so stupid?! How come I never noticed?!" The purple-clad genius yelled to himself, only to be interrupted by a knock at the door. 

"What's going on Don? What's withcha yelling?" Raph asked as he opened the door. "By the way, April got us Chinese a while ago. We saved some for ya." But Donnie whizzed by in a panic. "Where's Mikey?!" Raph then replied; "He just came back with Sensei. Why?" The red banded turtle asked as he set the food down, and Leo close by opened a fortune cookie. 

"'A huge secret will be revealed in your family'." Leo read out loud as Casey scoffed. "You listen to a cookie?"

At that, Mikey came in and Donnie imminently ambushed 'him'. 

"Mikey, did you know of your real gender? If you did, why didn't you say anything?!" Donnie asked/yelled at his younger sibling as he gripped Mikey's shoulders.

Mikey looked confused at first, but then gained a strained smile. "I was wondering how long you'd be able to figure it out since you're the smartest, but still, 10 years and now you noticed?" The orange turtle asked. "I'll be right back and explain. Or dad, do you want to start?" 

"I'll prepare them for the surprise while you do." Splinter assured his youngest child.

"Noticed what? What surprise?" Raph asked in agitation, not happy to be left out of a loop. 

"Master, did you know?" Donnie asked their father, ignoring Raph's question.

"Not until she was eight." Splinter said, as he sat down.

"She? Mikey's a male isn't he?" Leo asked, but he began getting a suspicious look on his face. 

"No, Sensei's right. I'm female." Mikey's voice popped up and the boys turned only to be absolutely shell-shocked at the sight of their little sister. 

She was still same, but she had curves in the right places that was no longer hidden by the bindings that also hid her rather ample chest. "Surprize, I guess?"

Casey looked to the fortune reading Leo still had before speaking; "Lesson learned; Never mock the cookie."

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Here's the first chapter!

I've noticed there aren't many TMNT 2014/16 stories involved with genderbenders but I took another swing at it.