Shego could also be the main antagonist. Maybe she discovers a way to time travel on her own and decides to go back in time to eliminate Kim before she becomes a threat. Kim would have to follow her through time to prevent this and save her younger self.
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.
It could be an evil scientist who wants to capture the cat girl for her unique abilities. Maybe he wants to use her enhanced senses or agility for his own malicious purposes.
A possible main antagonist could be a rogue scientist from Kim's world who has somehow gained knowledge of chakra and wants to use it to create an army of super - soldiers. He kidnaps some of Naruto's friends to study their chakra and it's up to Naruto and Kim to stop him.
Cell could be a great antagonist. Imagine Goten travels back in time to before Cell was complete. Cell could sense Goten's power and try to absorb him to become even more powerful. This would put Goten in a tough situation where he has to avoid Cell while also trying not to disrupt the timeline too much.
It could be a time - traveling villain who is trying to disrupt the timeline for their own gain. This villain might be trying to erase certain events or people from history to change the future in a way that benefits them.
It could be a time - traveling sorcerer who wants to change history for his own evil purposes and sees Achilles as a threat. The sorcerer might try to stop Achilles from getting back to his own time or use his knowledge of the future to his advantage against Achilles.
A time - traveling bounty hunter could be the main antagonist. He might be after Lucy because she has somehow disrupted the time - space continuum. He's cold - hearted and will stop at nothing to bring her to some time - traveling justice.
Perhaps an ancient evil that was sealed away long ago but is released due to Temari's time - traveling disruptions. This evil entity then starts causing chaos in the past, and Temari is the only one who can stop it with her modern skills and knowledge.
It could be a time - traveling villain from the future who wants to change the past to gain more power in their own time. They might try to stop Naruino from achieving their time - travel goals.
It could be a dark wizard from the past who has the power to manipulate time. This wizard might see Natsu and Mira as threats to his plans to change the past for his own evil gains. He would try to stop them from interfering with his time - related schemes.