Well, in such a fanfiction, Harry Potter might bring a new perspective to the Hellsing crew. He comes from a world where magic has different rules and ethics. His presence could lead to some internal conflicts within Hellsing as they debate whether to trust his 'alien' magic. Also, Harry might be shocked at the extreme measures Hellsing takes against vampires and other supernatural beings, and try to find a more 'humane' solution while still protecting humanity.
The plot could be that Naruto is somehow transported to the Hellsing universe. He starts off as an outsider but quickly proves his worth. His rasengan could be adapted to be effective against vampires, perhaps by infusing it with holy water or some other vampire - weakening element. Naruto's presence could also introduce a new dynamic to the relationships within the Hellsing organization, and he might even form an unexpected bond with Seras Victoria as they both have a strong sense of loyalty and a desire to protect the innocent.
Perhaps Harry joins Voldemort out of a sense of hopelessness. After seeing so much destruction in the wizarding world, he might think that joining Voldemort is the only way to end the war quickly. However, he soon realizes that Voldemort's methods are too extreme and tries to find a way to turn things around from within the dark side.
Well, one possibility is that Harry could use his magic skills in a discreet way to help the BAU team. For example, he could use a spell to make a suspect more talkative during an interrogation. Another could be that his experience with the dark arts and fighting Voldemort gives him an edge in understanding the motives of really evil criminals that the BAU might be hunting. He might also introduce the team to magical creatures that could be used as analogies for certain criminal behaviors.
In this fanfiction, Harry could be brought into the Unspeakables to deal with some ancient and powerful magic that has been awakened. He may start off as an outsider among the Unspeakables, but gradually earn their respect. His adventures within the Department of Mysteries could include uncovering long - lost spells and artifacts. This could also lead to a conflict between his loyalty to his old friends and his new responsibilities within the Unspeakables.
Well, one possible plot could be that Harry uses his magic skills in a covert way within the special forces. For example, he could use the Disillusionment Charm to make himself and his team invisible during stealth missions. He might also use his quick thinking, which he developed from all his battles at Hogwarts, to outwit the enemies. His ability to sense danger, much like his connection to Voldemort in the original series, could help the special forces avoid ambushes.
One possible plot could be that Harry Potter uses his magical skills to solve a case that NCIS is stumped on. For example, he could use the spell 'Revelio' to find hidden evidence that normal forensic techniques couldn't detect. His knowledge of the wizarding world might also lead him to suspect that a suspect is using some form of dark magic or enchanted object in their crimes.
Well, one possibility is that Harry is tricked into joining the dark side. Maybe Voldemort uses some dark magic to cloud Harry's mind and make him believe that the dark ways are the right ones. He could start using dark spells and turn against his friends.
Perhaps the story could start with Harry being in a desperate situation. He might think that joining the League of Doom is his only option to gain power to defeat a greater evil. However, once inside, he realizes the true nature of the league and has to fight against his new 'allies' to protect the wizarding world. He could use his knowledge of both the light and the dark magic he's exposed to within the league to his advantage.
The plot could involve Harry using his magic in the Stargate universe. Maybe he could use spells to help the Stargate teams in their battles against the Goa'uld. For example, a simple Stunning Spell could be very useful against the Jaffa warriors. He could also use magic to decipher some of the ancient technologies that the Stargate teams come across, since he has experience with ancient magic in his own world.
One possible plot could be that Harry is brought into the SG1 world because of a magical accident involving the Stargate. Once there, he realizes that there are dark forces at work in this universe too. He teams up with SG1 to find a way to get back home while also helping them to stop an impending invasion. Harry uses his Patronus charm to fend off some of the scarier alien creatures, and his knowledge of potions comes in handy when they need to cure a strange alien disease.