Another way is through shared villains. Say a villain has the ability to travel between the two universes and is causing chaos in both. This would force the heroes to come together. For instance, Loki could find a way to the Arrowverse and start causing trouble. The Arrowverse heroes would be out of their depth dealing with a god of mischief, so they call in the Avengers for help. The two groups would have to learn about each other's abilities and strategies to take on Loki.
Maybe the Flash could visit the MCU. He could race against Quicksilver. It would be a really cool showdown of speedsters from different universes. And then the Flash could get involved in an MCU - level threat, like Thanos' invasion but in a different timeline. He could use his speed to try and steal the Infinity Gauntlet from Thanos, creating a whole new plotline for a fanfiction.
The characters can be integrated through a common case. For instance, a murder that has forensic evidence only Brennan's team can handle and a mystery - writing angle that Castle is interested in. They would meet at the crime scene and start collaborating.
One way to integrate them is through a common enemy. Maybe a new villain emerges that has powers related to both the Twilight and Flash universes. The vampires and werewolves from Twilight could team up with the Flash and his allies to fight this enemy. They would need to learn about each other's abilities and work together. For example, the Flash could use his speed to distract the enemy while the Twilight characters use their super - strength or mind - control powers to defeat it.
For starters, you can focus on their skills. For instance, the Stargate characters' knowledge of different cultures and advanced technology can be paired with the Sentinels' unique abilities like their enhanced senses. Daniel Jackson from Stargate could study Sentinel culture, while a Sentinel could use their senses to help Jack O'Neill in combat situations.
The key is to find common ground. For example, both shows deal with the supernatural. So, a plot where a powerful supernatural entity threatens both the world of Supernatural and Mystic Falls would bring the characters together. Sam's knowledge of lore could combine with Bonnie's magic skills to fight this entity.
You can also integrate them through shared technology or concepts. For instance, the power source in the Halo universe could be related to some meta - human power in the DC universe. This could lead to a scientific exploration in the fanfiction where characters from both universes collaborate to understand and utilize this connection.
To integrate the characters well, start with their personalities. Mario is generally cheerful and brave, while Link is more stoic and determined. In a fanfiction, they could learn from each other. Link could teach Mario how to be more patient in combat, and Mario could show Link how to have more fun during their adventures. When it comes to the other characters, like Luigi and Zelda, they could have their own sub - plots. Luigi might be a bit intimidated by the more serious Hyrule environment at first, but then find his own way to contribute, just as Zelda could bring her wisdom to the Mushroom Kingdom.
The characters can be integrated in various ways. Danny could befriend Hiccup as they both have a sense of being different from their peers. Danny is a half - ghost and Hiccup was initially seen as an outcast among the Vikings. They could share their experiences of not fitting in. Astrid could be curious about Danny's powers and train with him, learning new combat techniques that combine Viking fighting skills with Danny's ghostly moves.
Some of the Pokemon could take on the forms of Undertale characters or vice versa. For instance, a Gardevoir could take on the appearance of Toriel to help comfort the other characters. This would not only be a cool visual but also a way to blend the two universes on a deeper level. The personalities of the characters could also influence the behavior of the Pokemon or the transformed characters. There could be a lot of emotional moments and comical situations as a result of these integrations.
The key is to find common ground in their abilities and personalities. For example, Captain America's sense of honor and leadership is similar to that of Obi - Wan Kenobi. They could lead a joint team in a battle. Just put characters with like - minded traits together and let their interactions unfold.