It could also be that Red Hood is being manipulated by a third party. This third party convinces Red Hood that Nightwing is a threat and needs to be neutralized. So, Red Hood kidnaps Nightwing, but as the story progresses, he starts to realize that he has been tricked.
One possibility is that Red Hood has some sort of vendetta against Nightwing. Maybe he blames Nightwing for something that happened in the past, like a mission gone wrong that affected someone close to Red Hood. So he kidnaps Nightwing to get revenge or to make him pay in some way.
His motivation could be related to a difference in ideology. Red Hood has a more brutal approach to crime - fighting compared to Nightwing. He might think that Nightwing's methods are too soft and by kidnapping him, he wants to force Nightwing to see things his way.
It's also possible that Nightwing and Slade end up having a long conversation during the captivity. Slade might try to convince Nightwing to join his side, perhaps by appealing to some sense of justice that he thinks Nightwing is missing. Nightwing, of course, would resist, but this could lead to some interesting character development for both of them as they debate their different ideologies.
In the fanfiction, Nightwing could be used by the Joker as bait to lure Batman into a trap. The Joker might have some elaborate and sadistic plan in store for both of them. Nightwing, being the strong - willed character he is, will likely try to resist the Joker's psychological games and attempts to break him while waiting for rescue.
It could be someone manipulating Red Hood. For instance, a powerful crime lord who has some dirt on Red Hood and forces him to kidnap Nightwing. So, in a sense, this crime lord would be the real villain.
In such a fanfiction, the plot might be centered around Red Hood having some sort of vendetta against Nightwing. Maybe he believes Nightwing has wronged him in the past, and the kidnapping could be a way to get revenge or force Nightwing to face something. For example, Red Hood could be trying to expose a secret that Nightwing has been hiding.
Well, one possibility is that Tim Drake might be extremely grateful and form a new alliance with Red Hood. This could lead to them working together to take on a bigger threat in the Young Justice universe. Maybe they'd start sharing intel and resources that they each have access to, which could give them an edge against their enemies.
Well, in a fanfiction like this, Naruto might be in for a tough time. Pan could be from some other universe and have her own motives. Maybe she wants to use Naruto's powers for her own gain. It could lead to a really strange adventure where Naruto has to figure out how to escape and get back to his own world.
One possibility is that Robin, being kidnapped, will have to rely on his own wits and skills he has learned from Batman. He might try to outsmart the Joker by finding weak points in the place where he is held captive. For example, if it's an old warehouse, he could look for ways to escape through the ventilation system or by using some tools he might find around. And the Joker, being the unpredictable villain, could be constantly taunting Robin, trying to break his spirit before Batman arrives.
First of all, the setting of the kidnapping is crucial. Is it in a desolate desert or a crowded city? If it's in a city, there might be more chances for Tim to signal for help. In this fanfiction, the outlaws could also have their own backstories that led them to kidnap Tim. For example, they might think Tim is involved in something that affected their group negatively. As the story progresses, Tim could discover some secrets about the outlaws that could either help him escape or make his situation worse.
Perhaps Itachi sees Naruto as a key to unlocking some hidden power or knowledge. He could be planning to train Naruto in some way, away from the influence of the village. This would be a strange turn of events considering their previous interactions.