One possible plot twist could be that the TMNT initially think the Young Justice team are enemies due to a misunderstanding. For example, they might see the Young Justice team using high - tech gadgets and assume they're working for an evil organization. Then, as they start to fight, they realize they have a common enemy and have to team up.
One common plot twist could be that Robin's injury was a setup by a hidden enemy within the Young Justice team. This would lead to a lot of internal conflict as the team members try to figure out who could have done such a thing.
One possible plot twist could be that the TMNT turn into dragons not because of some magic spell gone wrong, but because it's an ancient prophecy. They are the only ones who can save the city in their dragon forms from a powerful, otherworldly threat. As dragons, they have new powers like breathing fire or flying at supersonic speeds, which they use to fight the enemy.
A possible plot could be that Damian Wayne, while on a solo patrol, stumbles upon a Young Justice operation gone wrong. He steps in to help but is critical of their mistakes. This starts a tense relationship. As the story progresses, they are forced to work together on a larger threat that endangers not only Gotham but also the world. Along the way, Damian starts to understand the importance of friendship and trust within a team, which is something he hasn't really experienced before. And the Young Justice team also learns to see past Damian's prickly exterior and appreciate his skills and determination.
A possible plot twist is that the kiss is part of a prophecy. In the TMNT universe, there could be an ancient prophecy that foretold of a kiss between Leo and April which would either save or doom the world. So after the kiss, they start to discover clues about what this really means for them and their friends. Or perhaps the kiss is seen by an unexpected observer who then spreads false rumors about it, which leads to all sorts of misunderstandings within their community.
A common plot twist could be that April was actually kidnapped by someone she thought was a friend. This person could be under the control of a greater evil. It would add an element of betrayal to the story.
One possible plot twist could be that Mikey was kidnapped by an unexpected enemy, like a former ally who turned bad. Maybe it was someone he trusted, and this betrayal adds a layer of drama.
The TMNT's martial arts skills could be combined with Young Justice's superpowers in combat. For instance, if Robin's acrobatic skills are paired with Leonardo's swordsmanship, they could create some really cool and effective fighting maneuvers.
Well, in some fanfictions, a plot twist might involve the source of vengeance being misinterpreted. So, instead of the obvious villain being the target of vengeance, a new character emerges as the real cause of all the problems. This changes the whole dynamic of the vengeance and justice aspect. For example, a character might seem like a bystander but is actually pulling the strings behind the scenes, and when this is revealed, it turns the tables on who should be facing justice and who is actually in the right regarding vengeance.
One possible plot twist could be that Kiren is actually a long - lost relative of Naruto. This would completely change the dynamic of their relationship and add a whole new layer of complexity to the story. Another twist could be that Kiren is being controlled by an evil force, and Naruto has to find a way to break the control without hurting Kiren.
One possible plot could be that the failsafe is accidentally triggered. The Young Justice team then has to figure out how to stop it from causing more harm while also dealing with the immediate threats it creates.