One plot could be that Viper has a spell that can control minds, and she uses it on some of the Hogwarts students. Harry Potter discovers this and tries to find a way to break the spell. Loki, being the mischievous one, initially seems to be helping Viper but then has a change of heart and joins Harry to save the day.
Here's another idea. A powerful artifact is lost that can open portals between different dimensions. Harry Potter, Loki, and Viper are all after it for different reasons. Harry wants to keep it safe to protect his world, Loki wants to use it for his own amusement or power gain, and Viper wants to use it to bring chaos. Their paths cross as they search for the artifact, and they have to decide whether to work together or against each other.
A really unique plot would be if there was a magical tournament that included different realms. Harry Potter represents Hogwarts, Loki represents Asgard, and Viper represents some dark underworld. They all compete in various challenges, and along the way, they form unexpected alliances. Harry might learn some new skills from Loki, and together they try to outwit Viper in the tournament.