You could also do a crossover with 'Sherlock Holmes'. Alex Rider is on a case that Holmes has also been investigating. Alex's modern - day espionage skills and Holmes' deductive reasoning could combine in interesting ways. Alex might be able to provide the physical evidence that Holmes deduces from, and Holmes could help Alex see the bigger picture of the mystery.
One idea could be a crossover with the Resident Evil universe. Alex Mercer could find himself in Raccoon City during the zombie outbreak. He might use his powers to either fight the zombies or try to figure out what's causing the outbreak. Another idea is a crossover with the X - Men. Mercer's shape - shifting abilities could be an interesting contrast to the mutants' powers, and there could be a conflict or an alliance depending on the story's direction. A third idea is a crossover with the God of War series. Imagine Mercer in the world of Greek mythology, facing off against gods and monsters.
One idea could be an Alex Rider crossover with James Bond. Alex could be recruited by MI6 to assist Bond on a mission. They would bring their unique skills together, with Alex's youth and agility complementing Bond's experience and suave charm.
One idea could be that Alex Rider is sent on a mission that overlaps with a CHERUB operation. They initially suspect each other as spies from different agencies but then realize they can work together. Maybe they have to infiltrate a high - security facility that is involved in some sort of illegal arms trading.
A good antagonist could be a character from the 'Resident Evil' universe, like Albert Wesker. His superhuman abilities and evil plans for global domination would pose a huge threat to Alex Rider. Alex would have to use his wits and skills to stop Wesker's bio - terrorist plans.
One idea could be that Alex Rider is sent on a mission to Hogwarts undercover as a new student. He discovers the wizarding world while also trying to complete his MI6 task, which could be related to some dark wizard who has ties to a Muggle criminal organization. Another plot could be Harry Potter and his friends accidentally stumbling into one of Alex Rider's missions in the Muggle world and having to help him out using magic in a very discreet way. A third idea is that Alex Rider is revealed to have some latent wizarding abilities and he gets recruited by Dumbledore to help in the fight against Voldemort, bringing his unique set of spy skills to the wizarding war.
You could write a fanfiction where Alex Rider has to go undercover in a school as a normal student, but he discovers a secret society within the school that is involved in some sort of illegal activity. This would be a different kind of mission for him, as he's used to more international espionage. He would have to use his wits and skills in a more confined and familiar setting.
Well, I've read some where they start off as rivals. In this type of Alex Rider Crossover Cherub fanfiction, the two groups initially compete for the same objective, like getting hold of a crucial piece of intelligence. But as the story progresses, they realize they need to work together. It's a great plot device that can lead to some really exciting action scenes and character development.
One idea could be to explore what would happen if Alex Rider had to team up with a former enemy. Maybe they discover they have a common foe and must put aside their differences.
I think Ethan Hunt from Mission: Impossible would be a great addition. His high - octane action skills combined with Alex Rider's more stealthy approach would make for an exciting story.
One possibility could be that Alex Rider is on an undercover mission that somehow intersects with an NCIS case. Maybe he's tracking down a group involved in international espionage and they turn out to be linked to a crime on U.S. soil that NCIS is also investigating. For example, a terrorist organization that is smuggling weapons and using the sea routes which is NCIS' area of expertise. Alex could bring his unique skills in combat and infiltration, while the NCIS team offers their forensic and military investigation knowledge.