In the fanfiction, a powerful meta - human is stealing energy from various sources in both universes. Young Justice and The Flash join forces to track down this meta - human. Along the way, they learn from each other. For example, The Flash could teach some of the Young Justice members about speed - based combat techniques, while the young heroes could show The Flash new strategies for teamwork that he might not be used to in his solo crime - fighting.
One idea could be that a new villain emerges who has the ability to manipulate time, which affects both Young Justice's world and Central City where The Flash operates. The heroes from both groups have to work together to stop the villain before time is completely disrupted.
Perhaps there is a device that can open portals between different dimensions, and by accident, it links the world of Young Justice to The Flash's world. The Flash then teams up with the young heroes to find a way to close the portals before dangerous beings cross over. They face challenges as they try to understand each other's powers and ways of operating in their respective worlds.
A cool plot could be a time - travel related crossover. The Young Justice team travels back in time and meets the younger versions of the Justice League members. They have to work together to stop a time - traveling villain from changing history in a way that would destroy the future. Or perhaps there's a magic - based crossover where a powerful sorcerer is causing chaos. The Justice League, which is more used to physical threats, has to team up with the Young Justice, some of whom have magic - related powers, to defeat the sorcerer.
Well, you could do a story where the Flash family decides to take on a mentoring role for the entire Young Justice team, not just the speedsters. They teach everyone about the importance of quick thinking, not just quick running. It could be a story full of humorous moments as the Flash family tries to keep up with the different personalities on the team, and also some serious moments when they face a real threat that requires the combined skills of the Young Justice team and the speed and wisdom of the Flash family.
One idea could be that an ancient, powerful enemy emerges that the Justice League alone can't handle. Supergirl, with her unique Kryptonian powers and different perspective, joins them. She might introduce some Kryptonian technology or fighting techniques that give them an edge. For example, she could have a device that can neutralize the enemy's energy - based attacks.
One idea could be that the Young Justice team gets accidentally transported to an alternate dimension where the Justice League has turned evil. The Young Justice members then have to figure out how to reverse the situation while also evading capture from their once - heroes. Another could be a time - travel plot where the Young Justice team travels back in time and teams up with the early days of the Justice League to stop a threat that was thought to be long gone but has resurfaced in their own time. A third idea is that a powerful new villain emerges who can only be defeated by a combined effort of the Young Justice and Justice League, but first they have to overcome their differences in fighting styles and leadership.
One idea could be that Kid Flash returns with new superpowers. Maybe he was in some sort of other - dimensional training and now he can phase through time as well as objects. This would add a whole new dynamic to the team in 'Young Justice' as they deal with threats that require time - traveling abilities.
A more complex plot could be that there is a prophecy in both universes that foretells of a combined force from both Naruto's world and the Young Justice world being the only thing that can stop an upcoming great evil. This would lead to a series of events where characters from both sides have to learn to trust and work together. Naruto could bring his friends from Konoha, and together with the Young Justice team, they would train and strategize to face this ultimate threat.
One idea could be that the Outsiders are called in to help the Young Justice team when a new, powerful and mysterious villain emerges. This villain has a unique power that neither team has faced before, forcing them to combine their skills and resources.
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.
One idea could be that the two teams are forced to compete in a series of challenges by a mysterious villain. This would lead to some friendly rivalries and also force them to learn from each other's strengths. For example, the Teen Titans' experience with magic-based threats could help the Young Justice team, while Young Justice's strategic planning might be beneficial to the Titans.
One idea could be that Ghost Rider's powers are somehow needed to stop a demonic threat in the Young Justice universe. Maybe a powerful demon is causing chaos and the team realizes they need the unique abilities of Ghost Rider to send it back to hell. Another plot could involve a member of Young Justice being possessed and Ghost Rider having to help exorcise the demon while also teaching the team about the darker, supernatural side of their world.