Perhaps the Chaos Emeralds are hidden in different wizarding schools around the world, and in the fanfiction, a quest is set up for Harry Potter and his friends to find them all. Each emerald could grant a different ability, such as the power to control the elements, which could be used against the rising dark forces in the wizarding world.
Harry could use the Chaos Emeralds to boost his Patronus charm. The power of the emeralds might make his Patronus larger and more powerful, capable of warding off more Dementors at once.
In fanfiction, Mother Earth could be a hidden force that has been dormant for a long time. But due to some great imbalance in the wizarding world, she starts to awaken. Harry Potter might be the one to first sense her presence, maybe through a strange dream where he sees the earth itself calling out for help. Then, as the story progresses, he discovers that Mother Earth can communicate with certain wizards, and she imparts her wisdom to him to help him fight against the forces that are causing the imbalance, such as over - use of dark magic that is harming the natural world.
One way could be that the Infinity Stones are hidden artifacts in the wizarding world. Maybe they were created by an ancient and extremely powerful wizard long ago, and their powers are so great that they are feared and thus hidden. For example, the Time Stone could be related to time - turners, but with much more powerful time - manipulating abilities.
They could be a new magical invention by a young, brilliant Ravenclaw student. This student could be trying to find a way to help those with vision problems in the wizarding world. But the contacts end up having some unexpected magical properties, like changing color in the presence of certain spells or magical auras. Harry Potter could then get involved when he realizes that these contacts might be the key to solving a mystery related to a series of strange magical events happening around the school.
Venom's ability to heal quickly could also play an important role. In the Harry Potter series, injuries are common during battles and duels. A character with Venom's healing factor would have an advantage. They could survive attacks that would normally be fatal and keep on fighting. This could change the dynamics of battles in the fanfiction world. For example, if Harry was bonded with Venom, he could survive Voldemort's Killing Curse due to Venom's healing ability.
Medusa can be incorporated as a dark magic - created being. Maybe some dark wizard in the past tried to create a powerful weapon and ended up with a Medusa - like entity. In fanfiction, this could be the start of a new adventure for Harry and his friends as they try to stop this entity from causing chaos in the wizarding world.
In fanfiction, a Pegasus could be a symbol of great power or prophecy. It could be foretold that only a chosen wizard can tame a particular Pegasus, and this wizard will then be able to use the Pegasus's power to defeat a great evil that threatens the wizarding world. This would create an exciting plotline full of mystery and adventure.
Kirin could be incorporated by being a guardian of a hidden magical artifact in the Harry Potter universe. This artifact could be something that has the power to change the balance of magic. Harry and his friends might stumble upon the Kirin while searching for the artifact, and they have to earn the Kirin's trust to gain access to the powerful item.
The Infinity Stones could be linked to the Deathly Hallows. Maybe the Resurrection Stone has a connection to the Soul Stone. They could both have the power over life and death in different ways. And the other Infinity Stones could be related to the Elder Wand's power of domination and the Cloak of Invisibility's power to conceal, but on a much grander scale, if they were to be incorporated into the Harry Potter world.
Naruto could use the Chaos Emeralds to boost his speed. Just like how Sonic uses them to go super fast, Naruto could apply that speed to his movements during battles. This would make him even more unpredictable to his enemies.