One idea could be to have Ben Tennyson end up in the Young Justice universe by accident. Maybe his Omnitrix malfunctions during a fight and transports him there. He could then team up with the Young Justice heroes to fight a common enemy like the Light or some new villain that's a threat to both universes.
Well, one big challenge is getting the lore right. Warhammer has a ton of detailed lore, and Young Justice also has its own established universe. Combining them without messing up the facts is tough.
One idea could be that the Young Justice team has to prove themselves to the Justice League during a major alien invasion. The League initially doubts their abilities but as the battle progresses, they see the unique skills and teamwork of the young heroes.
Develop their relationships. Maybe a Young Justice hero has a huge crush on a Justice League member, which creates some interesting dynamics. Also, showing how they interact in battle, like a Young Justice member learning new combat techniques from a League veteran.
Sure. A lot of these crossovers play around with the different power levels and moralities. For example, a story could involve a Warhammer chaos warrior somehow ending up in the Young Justice world and causing chaos (no pun intended). It's all about how the authors blend the two very different universes together in an interesting way.
One great plot idea could be that the characters from Young Justice and Totally Spies are brought together by a common enemy. Maybe a powerful villain has a plan that affects both their worlds, like a device that can mind - control both superheroes and spies. So they have to combine their skills to stop it.
Maybe there's a villain who has the ability to cross between the dimensions of Danny's world and the Young Justice world. Danny and the Young Justice team have to combine their efforts to stop this villain. Danny could teach them about dealing with supernatural threats, while they could show him how to work better in a team setting in a more traditional superhero sense.
One popular 'Young Justice My Little Pony crossover fanfic' is 'Equine Justice'. It combines the action - packed world of Young Justice with the colorful and magical world of My Little Pony in an interesting way.
The telepathic abilities in Young Justice, like Miss Martian's, could be very useful for the Totally Spies when it comes to getting information from enemies. In return, the spies' disguise and infiltration skills could help the Young Justice characters get into places they normally couldn't. They could work together in a mission where the spies pose as normal people and the Young Justice characters are there as backup, using their powers secretly when needed.
Maybe there's a multiverse - related plot where the universes of Spider - Man and Young Justice start to merge. This causes chaos as characters from both worlds start to appear in the wrong places. The Young Justice team and Spider - Man have to work together to find a way to separate the universes again. They'd face challenges like dealing with different power levels and the cultural differences between their two groups.