One possible plot could be that the Kubikiribocho, the sword in Naruto, somehow finds its way into the Harry Potter universe. Harry discovers it during one of his adventures in the Forbidden Forest. He initially has no idea how to use it but gradually realizes it has some unique powers that can be harnessed against Voldemort. For example, it might be able to cut through dark magic spells. However, there are also some negative aspects to the sword as it tries to corrupt Harry a bit, just like the influence of the Horcruxes. Harry has to fight against this internal battle while also using the sword's power to defeat Voldemort.
Maybe the Kubikiribocho is a hidden relic in Hogwarts that was placed there long ago by a wizard who had visited the Naruto world. Harry stumbles upon it while exploring a secret chamber. The sword has a mind of its own and chooses Harry as its wielder. It gives Harry the ability to see the true forms of dark creatures, which helps him in his fight against Voldemort's Death Eaters. But it also has a thirst for blood, so Harry has to learn to control this aspect of the sword to use it for good without becoming a dark wizard himself.
Hermione could study the Kubikiribocho. She would pour over books in the Hogwarts library to figure out its origin and powers. Harry, on the other hand, might be the one to actually pick it up and test its abilities in combat. Ron could be a bit skeptical at first but would come around when he sees the sword's potential against the dark forces. For example, the sword might react differently to different spells cast at it. Harry could learn to use these reactions to his advantage in battles.
Maybe the Timekeeper is actually a descendant of an ancient wizarding family who was tasked with keeping time in balance. In the fanfiction, Voldemort discovers this and tries to use the Timekeeper's powers to go back in time and prevent his own downfall. The Timekeeper has to fight against Voldemort's minions while also trying to find a way to protect the timelines. Harry and his friends get involved when they notice strange time - related disturbances around the school. They join forces with the Timekeeper to stop Voldemort's evil plan.
In a fanfiction, the Triforce could be split among Harry, Ron and Hermione. Harry gets the Triforce of Courage, Ron the Triforce of Power (which he learns to use in a more responsible way), and Hermione the Triforce of Wisdom. Together, they combine their powers of the Triforce with their magic skills to defeat Voldemort once and for all. The Triforce's power could also be used to reform the wizarding world, bringing more equality and peace.
Well, perhaps the magical creatures from the Harry Potter universe end up in the '300' setting. Dragons could be used by the Spartans to fight their enemies. The centaurs could also join the battle, lending their archery skills. And Harry could learn some combat skills from the Spartans, which he could then use back in the wizarding world to fight Voldemort's Death Eaters.
Perhaps in this 'Harry Potter in Vegas' fanfiction, Harry accidentally apparates to Vegas instead of his intended destination. There he meets a group of American wizards who are using Muggle Vegas as a cover for a secret magic convention. Harry gets involved in a mystery where a powerful magical artifact has gone missing and he has to find it before it falls into the wrong hands.
A possible plot is that Tigger, with his boundless energy, teams up with Harry Potter. Tigger's unique ability to bounce high and far could be useful in Quidditch. He might bounce on the brooms and make them go even faster, or he could bounce around the Quidditch pitch, distracting the opposing team. Meanwhile, Harry could teach Tigger about the wizarding world and its secrets.
One idea could be that the characters from Persona 5 end up in the Harry Potter world. They could use their Personas to fight against the dark wizards. For example, Joker could use Arsene to take on Voldemort's Death Eaters.
In this fanfiction, Harry could be a boxer to raise money for the rebuilding of Hogwarts after the war. He travels to different wizarding communities to participate in boxing matches. Along his journey, he meets some old enemies who now also see the value in his cause. They form an unlikely alliance, and Harry's boxing skills become a symbol of unity and hope for the wizarding world.
One possible plot could be that Harry Potter somehow gets transported to Pandora. He discovers the unique flora and fauna there. Maybe he has to use his magic to communicate with the Na'vi or help them against a new dark force that has emerged on Pandora, similar to how he fought Voldemort in his own world.
One idea could be that Palpatine somehow discovers the wizarding world of Harry Potter. Maybe he sees it as a new realm to conquer. He could try to manipulate the Ministry of Magic using his Sith mind - tricks, and Harry Potter would have to figure out who this strange new threat is and stop him. It would be a clash of two very different kinds of magic.