A good plot could involve a villain from the Homestuck universe creating chaos in the Avengers' world. The Homestuck characters come to help, but there are misunderstandings at first between them and the Avengers. However, as they start to understand each other's powers and motives, they form a strong alliance to defeat the villain.
John Egbert and Spider - Man could be an interesting pairing. John's ability to manipulate wind and his generally positive attitude could contrast well with Spider - Man's quippy and more street - level heroics.
Maybe in the fanfic, Batman's rogues gallery somehow teams up with some of the Avengers' villains. This forces Batman and the Avengers to work together. Batman could introduce his unique gadgets and combat style to the Avengers, while they could show him their superpowers up close. For example, Iron Man could be intrigued by Batman's utility belt and try to create his own version of some of the gadgets.
One idea could be that the characters from Homestuck end up in the Underground of Undertale. They might have to deal with the various monsters there while also trying to find a way back home. Maybe John Egbert could team up with Frisk and they use their unique abilities to overcome challenges like puzzles and battles.
One idea could be to cross the Avengers with the X - Men. Imagine Wolverine and Captain America teaming up for a mission, their different leadership styles would create interesting dynamics. Another could be crossing them with the Harry Potter universe. Picture Iron Man trying to figure out how magic works in Hogwarts. Or a crossover with the Justice League, seeing Thor and Superman in a battle of strength would be epic.
Maybe the Sburb game from Homestuck starts to affect the Marvel universe. The Guardians of the Galaxy could be drawn into it, thinking it's some new cosmic threat. The Homestuck trolls' hemospectrum - related powers could interact in strange ways with the superpowers in the Marvel world. For instance, a high - blood troll's strength might be compared to that of the Hulk.
One idea could be that Nightwing is transported to the Avengers' universe through some sort of interdimensional rift. He then has to team up with the Avengers to fight a common enemy, like Thanos who has somehow acquired some of Batman's tech. Nightwing's acrobatic skills and detective abilities would be a great addition to the Avengers' power set.
One idea could be that Godzilla is drawn to the energy source of one of the Avengers' tech, like Stark's Arc Reactor. This causes chaos as Godzilla approaches the city where the Avengers are based. The Avengers initially see Godzilla as a threat and try to fight it. But then they realize that an even bigger alien force is using Godzilla's presence as a distraction. So, they have to find a way to communicate with Godzilla and work together to defeat the common enemy.
A really interesting plot could involve the Tesseract from the Avengers. It could be that the Tesseract has some sort of connection to the Darkness in SPN. When the Avengers are trying to protect the Tesseract, they accidentally release some of the Darkness. The Winchesters, with their knowledge of the supernatural, and the Avengers, with their superpowers, must then join forces to contain the Darkness again. The characters could also have some really fun interactions, like Dean being in awe of Iron Man's technology and Steve Rogers being impressed with Sam and Dean's hunting skills.
One idea could be that the Avengers have to deal with a supernatural force that is causing chaos in the city. Maybe it's a powerful demon that they can't defeat with their usual weapons and tactics. They then seek help from the Supernatural world, like Sam and Dean Winchester, who teach them about exorcisms and using holy water.
One idea could be that a powerful cosmic entity forces the Avengers and the Defenders to team up. They have to combine their unique skills, like the Avengers' high - tech gadgets and teamwork, with the Defenders' more street - level and magic - based powers to defeat this entity. For example, Doctor Strange from the Defenders could use his magic to create portals for the Avengers to quickly move around in battle.