I mentioned this in my intro, but I'll go more in depth with it since this forum is specifically for fan fiction. If you don't know much about Ninja Turtles, that's okay. I'm mainly asking for MLP advice since I'm new-ish to the series. I know the gist of it, like how Twilight became an alicorn and the Princess of Friendship. Mostly I'd like the advice of you, fellow bronies and pegasisters, in case I miss something or get something wrong.
With that being said, here's what I have so far:
In Equestria, Princess Celestia senses a powerful disturbance that could pose a threat to the ponies of Ponyville. Thirty moons have passed and the portal kept safely in Princess Cadence's castle is now vulnerable to any intruders who happen to pass through. Frightened, Princess Celestia calls upon all the princesses of Equestria and urges them to gather together and use their magic to hold a barrier so that no intruders can come through their world. When Princess Twilight hears of this, she's worried about her friends at Canterlot High, thinking they will have no means of protection with their side of the portal open. She tells Princess Celestia this and asks if she can put up a spell of some sorts so that no intruders can get in or out of Canterlot High's portal. Princess Celestia agrees and sends Princess Twilight on her way.
Waiting at Canterlot High is Sunset Shimmer, who Princess Twilight first informed of her visit. When she gathers the rest of the girls, Princess Twilight lets them know what's happening and they all ban together to build a barrier for the portal. However, before they can start the spell, the Kraang manage to come through the portal. Though they don't see much potential in the world of Canterlot High, they notice Princess Twlight's powerful magic and feel as though she will become useful in their invasion. Princess Twilight is captured.
Unsure of what to do, the girls decide to follow Princess Twilight and her captors, but are immediately stopped by Canterlot High's own Twilight Sparkle (the one at the end of the credits in Rainbow Rocks). Confused of their being two Twilight's, the girls order an explanation from Canterlot High's Twilight. She tells them she knew something like this was going to happen after all the magical occurrences that have been happening at Canterlot High and figured erasing everyone's memories would do the trick in keeping them safe. Unsure of what she's talking about, the girls demand a a further explanation, so Twilight takes them to her home. She explains that Canterlot High once held magic just like that of Equestria, but not as powerful. Everyone was a hybrid of their pony counterpart in Ponyville, but ever since the incident with Sunset Shimmer and the Sirens, the magic at Canterlot High has become stronger and more known, leaving them a target for outsiders, such as the one that stole Princess Twilight. To keep from such a thing happening, Twilight was ordered by Principal Celestia and Vice Principal Luna to erase everyone's memories and have everyone think they were all just normal high school students. It worked for a while until the incident with Sunset Shimmer and the Sirens, opening everyone's memories of the magic they once possessed.
Worried about Princess Twilight's fate, the girls decide to follow the Kraang anyway so that they could rescue their friend, figuring the magic they possess now will be enough to keep them safe. Thinking their plan is a suicide mission, Twilight forbids them from entering the portal, but the girls urge her to come along with them because of her knowledge with the portals. Not wanting them to get hurt, Twilight begrudgingly follows.
So far, that's all I've got. I'm thinking the Kraang use Princess Twilight's magic to gain control over the humans so that they become more "compliant" with the invasion and the mutation of New York City. As for the mane, er, five in this case, Sunset Shimmer, and Twilight running into the Turtles, I'm thinking they run into Raph and Casey first after trying to fight against some Kraang soldiers and losing horrifically when they realize their magic doesn't work in this realm. (As to why their magic doesn't work, I'm going with their magic works differently in different dimensions. If anyone has a better idea, please feel free to voice your thoughts. )
After Casey and Raph lead them out of harms way, the girls ask the two if they know anything about the Kraang. Raph and Casey are hesitant to tell them anything, which angers the girls and they try to pursue the Kraang on their own. Not wanting them to get hurt, Casey offers to have the girls follow them to April's apartment, much to Raph's disapproval.
For those who are familiar with TMNT, this is taking place during The Invasion pt. 1 and pt. 2. I'm not sure if I want it to go all the way through both episodes with them saving Princess Twilight in the end, but being stuck in New York City or them just not being able to save Princess Twilight and having to escape to Northampton with the Turtles, April, and Casey. Any form of advice will be much appreciated. I can't wait to get this story all worked out and ready to post on FF.net and possibly FiMfiction.net!