Another possibility is that the Fairy Godmother has an evil sister. She is jealous of the happiness that Shrek and Fiona have found and decides to take it away by harming their babies. She could use her fairy magic in devious ways to bring misfortune to the ogre family.
Perhaps it's a new character, like an evil wizard who has heard about the power of Shrek's family. He believes that by getting rid of the ogre babies, he can gain control over the swamp and all of Far Far Away. So he devises various evil plans to harm them.
One possible plot could be that the ogre babies fall ill due to a magic spell gone wrong in the swamp. The spell could have been cast by a vengeful fairy who was angry at Shrek for some reason. Shrek and Fiona then have to go on a journey to find the antidote to save their babies.
An ancient and evil force that was once sealed away but has been awakened by the birth of the baby dragons. This force is drawn to the pure and powerful energy of the babies and wants to corrupt them. It uses dark magic to try and influence the babies' minds, and Toothless and Light Fury have to fight this powerful and mysterious foe to protect their young.
It could be an evil fairy who was exiled from the fairy - tale world long ago. When Cory enters the Shrek world, her magic senses pick up on his 'foreign' energy. She sees this as an opportunity to get revenge on the fairy - tale world. She tricks Cory into helping her, making him think she's good. But once he realizes her true intentions, he has to team up with Shrek and his friends to stop her from casting a dark spell that would plunge both worlds into eternal darkness.
Hawkmoth is an obvious choice. His whole mission is to obtain the Miraculouses, and in a death fanfiction, he could succeed in a more devious way than in the original series, directly or indirectly causing Ladybug's death.
Danzo could be the main villain. He is known for his underhanded tactics and his dislike for Naruto. He might see Naruto as a threat to his power and plan to get rid of him by leaving him in the Forest of Death. Danzo could have manipulated some other characters to make it seem like it was a legitimate mission gone wrong.
Perhaps a new character could be the main antagonist in this fanfiction. A power - hungry alchemist who discovers the Turtles' mutation and wants to use their baby forms to create an army of mutant slaves. This alchemist would stop at nothing to get his hands on the baby Turtles and experiment on them.
Lex Luthor could be a likely candidate. He is extremely intelligent and has a long - standing vendetta against superheroes. He might come up with a complex plan using his vast resources and scientific knowledge. For example, he could create a weapon that targets their unique abilities. He could also manipulate other villains and heroes alike to create a situation where Batman and Wonder Woman are isolated and vulnerable.
Another possibility could be Sakura. She could be adopted into the village, perhaps because of her medical skills. In the village, she could learn new ways to combine her medical ninjutsu with the Oni Ogre's knowledge of natural healing. Her strong - willed personality would help her assert herself in this new environment.
Most likely Harry Potter himself would be one of the main characters. After all, it's in the title related to the Harry Potter world. And of course, the ogre would be a main character too as it's a key part of the fanfiction.
Another possible antagonist could be an alien scientist who was involved in the creation or discovery of the Necrofriggian babies. This scientist might have his own evil plans for the babies and sees Ben as an obstacle in his way. He could be using his advanced technology to try and capture the babies from Ben.