Another potential antagonist could be Ra's al Ghul. He has always had an interest in Batman and his allies. Maybe he sees Robin as a key piece in some grand scheme for Gotham's future or his own immortality project and has taken Robin away.
The most obvious antagonist could be the Joker. He loves to torment Batman, and kidnapping Robin would be a great way to do that. He might have some elaborate plan to break Batman's spirit by harming Robin.
The Joker could be a great antagonist. He might have captured Robin for his own twisted games and is holding him hostage in some elaborate death - trap. The Young Justice team would then have to outwit the Joker to get Robin back.
Well, Batman could start by gathering all his allies in the Bat - family. He would call on Nightwing, Batgirl, and Alfred for support. They could work together to track Robin's whereabouts. Maybe they find clues that lead them to an abandoned lair deep in the sewers of Gotham. There, they have to fight through a horde of thugs to reach Robin.
The main antagonist could be a deranged chemist who was once shunned by the scientific community. He uses his knowledge of chemistry to create deadly toxins and gases to get revenge on those who wronged him. He sees Batman and Robin as obstacles in his path of destruction.
Lex Luthor could be a great main antagonist. He could be jealous of the trio's popularity and see them as a threat to his own power - hungry plans. He might create elaborate traps and use his vast resources and intellect to try and take them down, all while trying to make it look like they are the bad guys in the public eye.
The Riddler could be a great antagonist. He could set up puzzles and traps all over the city that is now Robin's jungle gym. Robin would have to solve the riddles to avoid the traps while still using the urban jungle gym to his advantage.
The antagonist could be a new, self - proclaimed ninja god who wants to rule over all the villages. He sees Naruto as the only threat to his power, so he used a powerful spell to take away Naruto's godlike abilities. Konoha wants Naruto back to stop this tyrant. This antagonist might have an army of brainwashed ninja at his command.
How about Ra's al Ghul? He has his own ideas about justice and order that are very different from Batman's. He could see Robin as a potential recruit for his League of Shadows. Ra's al Ghul could manipulate events to make Robin question Batman's methods and try to draw Robin to his side.
Well, in this fanfiction, perhaps Robin left because of some misunderstanding with the team. The Young Justice team then starts to recall all the great things he did for them. They search everywhere, from Gotham to other far - flung places. They might even encounter new allies or enemies during their search for Robin. As they get closer to finding him, they also start to resolve the issues that led to his departure in the first place.
A new, self - made villain who is obsessed with colors and wants to collect all the 'powerful' colors in the world. Robin's red stands out to him as one of the most important ones to obtain, so he sets out to defeat Robin and take his red essence.
The Joker could be a likely antagonist. He might be causing chaos in Gotham, and Robin has to hide in Batman's cape to avoid being spotted by him. The Joker's unpredictable nature would add tension to the story.