Brother Eye could be a possible main antagonist. If it were to gain the ability to time - travel, it could try to rewrite history to create a world where it has complete control. It could manipulate events in different eras to eliminate any threats to its dominance, and Batman Beyond would have to stop it from achieving its goal.
A new villain created specifically for the time - travel story could be interesting. This villain could be a time - traveling bounty hunter who is after Batman Beyond for some reason. Maybe he has been hired by a future organization to stop Batman from interfering with their plans in the past or future. He would have advanced time - travel technology and combat skills, making him a formidable foe for Batman Beyond.
Ink could be a great antagonist. He has the ability to manipulate his body into various weapons and forms. He could be seeking to take over Gotham's underworld in the 'Batman Beyond' era and sees Nightwing and Batman Beyond as threats to his plans.
The Riddler could be a great main antagonist. He could use his knowledge of time paradoxes and puzzles to try and outwit Batman as he travels through time. He might set up elaborate traps across different time periods that Batman has to solve.
Terry McGinnis could face off against a time - traveling Ra's al Ghul. Ra's al Ghul has always been obsessed with immortality and the betterment of the world through his own extreme means. If he had the power of time travel, he could try to reshape history to his liking, which would put him directly at odds with Batman Beyond. Ra's al Ghul's long - term plans and strategic mind would make for a complex and engaging conflict.
Ink could be a great main antagonist. He has the power to manipulate shadows and could use this ability to create chaos in Gotham and beyond. He might target the Justice League and Batman Beyond because they represent order and he wants to spread his own brand of darkness.
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.
The Batman Who Laughs could also serve as the main antagonist. He represents a twisted version of Batman, and his goal could be to infect all the Batverses with his madness. His knowledge of Batman's tactics and his own insanity would pose a huge challenge for the normal Batman as he tries to stop him from spreading chaos.