One idea could be to have the wizards from Harry Potter's world discover the Stargate Atlantis technology. Maybe they could use magic to help repair or understand some of the advanced technology in Atlantis. For example, Hermione could use her vast knowledge of spells and ancient runes to decipher the Atlantis control panels.
A more complex fanfic could be about a dark wizard getting access to the Stargate Atlantis technology and trying to use it for evil purposes. The heroes from both worlds, like Harry Potter and the Atlantis team, would have to team up to stop him. They would need to combine their skills, magic and technology, to overcome the threat. This could lead to some really interesting battles and interactions between the two groups.
One idea could be to have the characters from RWBY travel through a stargate to the Pegasus Galaxy where Stargate Atlantis is located. They could encounter the Wraith and have to use their unique abilities from Remnant to fight them. For example, Ruby's speed and Crescent Rose could be very useful in combat against the Wraith.
A fanfiction could involve a character from Atlantis having some sort of magic ability, similar to the wizards in Harry Potter. This character could travel to the wizarding world and learn about their magic, and in turn, teach the wizards about Atlantean technology. For example, they could show the wizards how to use some of their advanced healing devices.
Perhaps a character from the Stargate Atlantis world could have some latent magical abilities. This discovery could lead to them being sent to the Harry Potter world to learn more about magic. In turn, wizards from the Harry Potter world could be intrigued by the technology in Atlantis and travel there to study it.
One idea could be a story where a Wendigo somehow enters the wizarding world of Harry Potter. Maybe it's brought in by a dark wizard who wants to use it as a weapon. The Trio - Harry, Ron, and Hermione - would then have to figure out how to defeat it using their magic and knowledge.
One idea could be that Hulk somehow gets transported into the wizarding world of Harry Potter. Maybe a magical experiment gone wrong by a Hogwarts student creates a portal that sucks Hulk in. He could then cause chaos as he's not used to the magic and strange creatures there.
There might be a fanfiction where the characters from Harry Potter are somehow transported to the world of Stargate Atlantis. Harry, Hermione, and Ron could find themselves in a completely different environment, having to learn about the Pegasus Galaxy and its threats. Maybe they would use their magical skills to fight off the Wraith. It would be a great story of two different fictional universes colliding and the characters having to adapt to each other's worlds.
Another concept is that the magic from the Harry Potter series starts to seep into the DC universe where the Justice League operates. This causes chaos as the laws of physics in the DC world are disrupted. The Justice League has to seek help from Hogwarts professors to understand and contain this new form of magic energy. Superman might be intrigued by the idea of magic being a new power source or a new threat he can't easily overcome with his super strength.
One idea could be that Tony Stark somehow discovers the wizarding world while working on a new technology. Maybe his sensors pick up some strange magical energy. He then meets Harry Potter and they team up to face a new threat that combines magic and technology, like a dark wizard using Stark Industries' tech for evil purposes.
One idea could be a fanfic where Harry Potter discovers a hidden portal in Hogwarts that leads him to the time of King Arthur. He could use his magic skills to assist Arthur in battles, perhaps using spells to defeat the enemies that Arthur's knights struggle with. For example, Harry could use the Stunning Spell to incapacitate a large group of invaders.
One idea could be to have nanomachines in the Harry Potter universe that are secretly created by a dark wizard. They could be used to control the minds of students, but the protagonists discover this and use magic inspired by LotR spells to combat it. For example, a Patronus charm with a LotR - like incantation to repel the nanomachine - influenced dark magic.