They might form an alliance when they suspect a certain student or group of students of being under the influence of a dark magic object. Harry and Neville could use their combined skills, Harry's courage and Neville's knowledge of plants (which could be useful if the object is related to a plant - based dark magic), to investigate and neutralize the threat.
Perhaps they form an alliance to research and understand some long - forgotten magic in the Hogwarts library. This could lead them to discover a powerful spell that could help in the fight against Voldemort later on. They would have to work together to decipher the ancient texts.
One idea could be that Harry and Neville form an alliance to secretly train students in advanced defensive magic outside of Umbridge's notice during her reign at Hogwarts. They could use the Room of Requirement as their base.
Another plot could be that Harry and Neville are actually long - lost twins separated at birth. They start having strange dreams about each other and then figure out the truth. This revelation would change their relationship and how they see themselves in the wizarding world. They could then team up to face a new, powerful dark force that is emerging, using their combined skills and the new - found bond between them.
One idea could be a crossover where Harry and Neville end up in the Naruto universe. They could learn chakra techniques and use their magic in new ways. For example, Harry might combine his Patronus charm with a chakra-based attack. Neville could use his knowledge of Herbology to discover new medicinal plants in the Naruto world.
One idea could be a new dark wizard threat that forces the characters from different houses to form an even stronger alliance than before. They might have to combine unique spells and strategies that each house is known for.
Maybe a fanfic about how Harry and Neville become best friends during a particularly difficult year at Hogwarts. They support each other through exams, Quidditch matches, and dealing with bullies like Draco Malfoy. Neville could help Harry with his Herbology studies, and Harry could teach Neville some useful Defense Against the Dark Arts spells.
One idea could be that Neville discovers a magical potion that enhances muscle growth as part of a Herbology experiment gone wrong. This causes him to rapidly gain muscles and he has to figure out how to control this new strength. He might accidentally break things around Hogwarts at first, but then learns to use it for good, like in a Quidditch match where he uses his strength to save a player from a dangerous fall.
One idea could be that the marriage law forces Hermione and Neville to get married, but at first they are hesitant. However, as they start to live together, they discover each other's hidden talents. For example, Neville shows his amazing skills in herbology which Hermione admires. They gradually fall in love as they face challenges together, like dealing with the expectations of their friends and family who had different ideas about their relationship.
Bellatrix Lestrange could also be a great antagonist. She could target their alliance as she is loyal to Voldemort. She might try to capture them to use as bait for other Order of the Phoenix members or to simply gain information about their plans to resist the Dark Lord.
One idea could be a story where a group of humans and Covenant members are forced to team up against a new, greater threat that endangers both their species. Maybe a powerful alien race that neither has encountered before.
In some fanfictions, their twin status might change the way the Sorting Hat sorts them. Instead of Harry going to Gryffindor, perhaps they both end up in Hufflepuff because of their shared values that are more in line with that house. This could lead to a completely different story arc where they are known for their loyalty and hard work rather than Harry's typical Gryffindor - like heroics. Also, their family relationships would be different. The Dursleys might have to deal with two magical children instead of one, which could change the way Harry (and Neville) grow up and view the Muggle world.
In some fanfiction, they could be on a quest to find a hidden magical artifact that was once owned by a great wizard. Along the way, they encounter various magical creatures and overcome obstacles using their combined skills and courage. Neville's knowledge of Herbology and Harry's combat skills would make them a great team. For example, Neville could use his knowledge of plants to create barriers or distractions while Harry battles any dark wizards or dangerous creatures that try to stop them.