The story began with Twilight S. who wanted to make a modification to the portal that communicates Equestria and the human world. She wanted to make the portal able to "track" the location of her friends, and allow her to always appear near them instead of relying in fixed locations, such as the CHS statue or the naturally occurring portal in the tropical island. She modified the portal with a "space" add-on. Then she also wanted to force the portal to stop "adapting" the users biology to that of the destination world. Twilight wanted to appear in her normal alicorn self to her friends. Thus, she added a "essence" add-on, based on Queen-Novo's pearl, to help her keep her shape while traveling between worlds. She didn't count that the portal had several safeguards and her messing with it caused a malfunction that sent her to the human world. Yes, tracking the location of her friends, yes, making the portal not dependant on a fixed asset, but now the "essence" modification went awry, and since she appeared in the ocean, the portal adapted Twilight and turned her into a mermaid, and since the magic is unstable, it spreads via touch, effectively making "contagious mermaids".
So, Twilight found Pinkie and touched her, and to her horror, Pinkie became a mermaid, then the latter touched Rainbow Dash, who didn't like it AT ALL, and then she, in turn hunted Rarity and grabbed her to make the fashionista lose her legs, then Rarity in panic tried to escape and found a free-diving AJ and in an attempt to get help from said farm-girl, she ended up "infecting" her with the mermaid course. AJ went to shore looking for help, grabbed her clothes and Pinkie's scooter and drove around town until she arrived to the AirB&B they all were renting for the vacation. She found Fluttershy in the driveway, whom lifted AJ from the scooter and tried to take her inside to a bathtub (you know, AJ being now a mermaid and all) only to end up transformed herself into a type of mermaid that can not breath very well in the air (unlike AJ and Pinkie). They rush back to the ocean, but they are chased by the police, who received the report of a stolen scooter. They crash the scooter on the water, they have to explain the situation, lift the charges. Meanwhile Rainbow Dash has gone rogue and fought against Rarity (who was tasked with helping keep her out of trouble).
RD, now convinced that she will never be a human again, goes about turning folk into merfolk, only to find that the transformees kinda enjoy the change (conveniently hides the fact that nobody knows if it is permanent) Her first victim is Trixie, who then goes and finds her friends The Illussions and they willingly join her magician friend under the sea (pun very intended). Fluttershy and Rarity and Twilight go and try to stop both RD and find that Trixie and the Illussions are now turned too. They decide to "convince" RD to come back to reason. All the while, Sunset Shimmer and Sci_Twi have been put up to speed of the situation too, and both genius girls try to find a way to revert their friends back to normal, they go and disguise themselves as their former villain selves to stea…. (I mean… borrow, that is… borrow!) several technological items from a Villain-Con.
All the while, Pinkie and AJ are still at the pier from which AJ crashed the scooter, and now they pulled it out of the water and are repairing it. Of course, some street vendor has come and is offering some cookies from a "farm that remembers".