One idea could be Sonic and Shadow having to team up to save a new character that has a special power that could be misused by the bad guys. They start off not getting along during the mission but gradually learn to respect each other's skills.
A plot could revolve around Sonic and Shadow being framed for a crime they didn't commit. They are on the run from the authorities and other characters who believe they are guilty. As they try to clear their names, they discover that there is a larger conspiracy at play, involving an old enemy who is trying to turn everyone against them. Along the way, they have to face their own differences and learn to trust each other completely in order to expose the real culprit.
Perhaps there could be a plot where Sonic and Shadow are in a relationship, and Shadow becomes pregnant unexpectedly. They then have to face the reactions of their friends and foes alike. Some friends might be supportive, while foes could try to use this as a weakness against them. And they have to navigate through the challenges of preparing for a new life while still being heroes.
One idea could be that they have to team up to stop a new powerful villain who is causing chaos across different zones. This villain could be creating some sort of energy disruptions that only their combined powers can counter.
One idea could be that Sonic Underground's siblings get separated in a new zone and Shadow accidentally stumbles upon them. He initially thinks they are enemies but then realizes they are on the same side against a common foe. Another could be that Shadow is on a mission related to the Chaos Emeralds and crosses paths with Sonic Underground. They end up having to team up to stop a new villain who wants to use the power of music and the Chaos Emeralds for evil.
One plot idea could be Dark Sonic having to face a new villain that is even more powerful and is threatening to destroy his world. He has to find a way to control his dark powers even more to defeat this foe.
A possible plot for 'sonic meets sonic boom fanfiction' is that a strange rift in the dimensions brings Sonic and his friends from the classic Sonic world into the Sonic Boom world right when they are about to have a big celebration. However, the Sonic Boom characters are initially suspicious of these new arrivals. But as they start to realize that a common enemy is behind the rift, they join forces. Sonic and Sonic Boom Sonic could have a friendly competition to see who can defeat the most badniks during the adventure, which also helps them bond and understand each other's strengths better.
One idea could be Sonic discovers a magical land where all the characters are in an abdl state. He has to navigate this new world while also dealing with his own changed circumstances. For example, he might have to learn to control his new abilities that come with this state.
In some fanfictions, they might explore the differences in their personalities. For example, Classic Sonic's more simplistic and straightforward approach contrasted with Modern Sonic's more complex and sometimes cocky attitude. They could start off not getting along due to these differences but then learn to work together. Maybe there's a story where they are both trapped in a strange dimension and have to rely on each other's skills. Classic Sonic's spin - dash and ability to handle more 2D - like terrains, while Modern Sonic can use his homing attack and boost in the more complex 3D areas of the dimension.
One idea could be that Sonic from Sonic X accidentally travels to the Sonic Boom universe and has to adapt to the different environment and new versions of his friends. Maybe he teams up with Sonic Boom Sonic to defeat a common enemy that has found a way to cross between the two universes.
Another plot idea is to create an alternate timeline within the 'a walking shadow' world. This could involve different events happening to the characters, leading to new relationships and challenges. For example, a character who was once an enemy could become an ally in this new timeline.
For Shadow of the Colossus fanfiction, you could write about a hidden society within the Forbidden Land. They worship the colossi in a different way than the main narrative implies. Wander stumbles upon this society during his journey. Or, you could do a fanfic where the colossi are not actually the 'bad guys'. They are guardians of something far more important and Wander is being used by the shadowy forces that sent him on this quest. And finally, a story about how the magic or energy that powers the colossi affects the wildlife in the Forbidden Land in ways not shown in the game. For instance, there could be mutated or super - intelligent animals due to this energy.