Maybe the main antagonist is an old enemy of Robin's who becomes jealous of his new powers. This enemy then devises a plan to steal Robin's powers or at least neutralize them so that he can regain his former status as the top threat. He could be a powerful martial artist or a criminal mastermind with a large network of henchmen.
There's a possibility that the main antagonist is a supernatural being. For example, a demon who sees Robin's new powers as a threat to his own dominion. The demon could try to corrupt Robin and use his powers for evil purposes. He would use his own dark magic and minions to try and bring Robin down to his side.
Perhaps a powerful sorceress. She could be jealous of Robin's connection to Batman and the other heroes, so she uses her magic to turn Robin into a girl as a way to humiliate and weaken him. The sorceress could then try to use Robin's new form to her advantage, like trying to make Robin turn against the heroes or something.
A new character could be introduced as the main antagonist. Maybe a powerful alien who sees Kim's new powers as a threat to his plan of taking over the earth. This alien could have his own set of powers that are quite different from Kim's, like the ability to control minds. Kim would have to not only learn to use her new powers but also find a way to defeat an enemy with such a dangerous ability.
A dark entity from another dimension could be the main antagonist. It senses Anna's new powers and wants to use them to open a portal between dimensions so that it can bring its army of monsters into Anna's world. So it constantly hunts Anna down, trying to either force her to use her powers for its own evil plan or simply kill her and take the powers for itself.
It could be another character who is jealous of Lucy's new powers. Maybe a classmate or a rival in her community who wants those powers for themselves and will do anything to take them from Lucy.
In this fanfiction, Robin might get powers as a result of a genetic mutation triggered by a rare chemical. These powers could include enhanced speed and the ability to see in the dark. He initially hides his powers from the team because he's afraid of how they'll react. But when a dangerous situation arises where his powers could be the key to victory, he reveals them and they all work together to defeat the enemy and accept his new status.
Another possibility is that one of Leo's classmates becomes jealous of his powers. This classmate could start spreading rumors about Leo, trying to turn everyone against him. Eventually, the jealousy could turn into something more sinister, and the classmate could team up with some bad elements to try and take away Leo's powers.
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.
It could be another person who also has some sort of mind - controlling abilities and wants to use the boy's powers for their own evil plans. This antagonist might try to trick the boy into using his powers in the wrong way.
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.
It could be a jealous rival. Maybe someone who has always been envious of Robin's abilities or popularity. Now that Robin is in a more vulnerable state as a girl, this rival sees an opportunity to undermine him.