In a fanfiction, Shadow could lose his memory and end up in the My Little Pony world. The ponies take him in and help him regain his memories. Along the way, he forms bonds with different ponies. For example, he might befriend Twilight Sparkle who is interested in his unique abilities and tries to use her magic to help him. As he slowly remembers who he is, he has to decide whether to stay in this new world of friendship or return to his own world.
One idea could be that Shadow somehow gets transported to the My Little Pony world. He might initially be a bit of an outcast due to his different and edgier personality compared to the ponies. But as the story progresses, he could learn about friendship and harmony from them and in turn, teach them about his own values like loyalty and justice in a different sense.
One idea could be that the Omnitrix somehow gets mixed up with the magic of the sirens. Ben, as one of his alien forms, has to deal with the alluring powers of the sirens in the My Little Pony world. Maybe he has to stop them from using their voices to take over Equestria while also not getting charmed by them himself.
A more complex idea could be that there's an alternate universe where the villains from both worlds combine forces. The Green Goblin teams up with Discord. In this fanfiction, Spiderman and the Mane 6 have to put aside their differences in fighting styles and cultures to defeat this powerful alliance. They learn from each other's strengths, with the ponies teaching Spiderman about the magic of friendship and Spiderman showing them some cool combat moves.
They can co - exist if there is a common goal. For example, if a powerful and evil force threatens both Shadow's world and the My Little Pony world. They would have to work together to defeat this enemy. Shadow could use his combat skills and speed, while the ponies use their magic and friendship power.
A great plot for Shadow the Hedgehog game fanfiction could involve Shadow's relationship with other characters. For instance, a story about how he forms an unlikely friendship with a young and naive creature in the Sonic world. He then has to protect this new friend from the chaos and danger that constantly lurks in their world. This would show a different side of Shadow, his more protective and caring side.
One idea could be that Shadow somehow gets transported into the Harry Potter world. He might use his speed and combat skills to help the students at Hogwarts during a time of great danger, like when Voldemort's forces are attacking. Maybe he teams up with Harry and they learn from each other's fighting styles.
One idea could be that Shadow discovers he has vampire-like abilities after a strange encounter in a dark, enchanted forest. He then has to struggle with his new thirst for blood while still trying to protect his friends and the world from villains.
One interesting crossover could be Sonic's speed being used to help the ponies in Equestria in a time of crisis. Maybe he races to deliver an important message across the land faster than any pony could.
One plot idea could be that Shadow and Amy are on a mission together to save Sonic who has been captured by a new villain. Along the way, they start to understand each other's motives and personalities better. Amy's positive attitude might start to rub off on Shadow, who is usually more brooding.
One idea could be a story where Sonic accidentally runs into the My Little Pony world. He could team up with Twilight Sparkle to stop an evil force that's threatening both their worlds. Maybe a chaos - causing villain has found a way to cross between the two realms.
One idea could be that the ponies from My Little Pony end up in the world of Skyrim. They could use their unique magical abilities to interact with the various races in Skyrim. For example, a unicorn pony might be able to use its magic to heal the wounded in Skyrim's battles, much like a Restoration spell in the game.