In some cases, a future villain could be the main threat. For example, if they travel to the future and there is a new dark wizard who has risen to power. Teddy and Harry would have to figure out how this new villain came to be and try to stop their evil plans.
Voldemort could still be a main villain. Imagine if Teddy and Harry travel back in time and Voldemort discovers their presence. He might see them as a threat to his plans and try to eliminate them. This would lead to a lot of dangerous encounters and battles.
It could be a dark wizard from the past who somehow senses that Harry and Teddy don't belong in that time and tries to use their presence for his own evil gains. Maybe he wants to steal their future knowledge to become even more powerful.
It could be an ancient dark wizard who was trapped in a time - locked state but is now released due to the time - traveling disruptions caused by Harry and Teddy. This wizard might see them as threats to his own dark designs on the wizarding world and try to eliminate them.
It could be a dark wizard from the past who senses Teddy's anachronistic presence and tries to use his time - traveling knowledge for evil. Maybe a wizard who was on the verge of creating a really dark magic but was stopped in the original timeline, and now with Teddy's interference, he gets a second chance.
The Emperor could still be a main villain even in a Padme time travel fanfiction. If Padme travels to a time when the Emperor is already in power, he would surely oppose her as she represents a threat to his rule. He might try to manipulate events to keep her from changing the future or past, depending on where she travels to.
When they travel to the future, a powerful corporation or a group of people in control of the new world order could be their enemies. These entities might not want Teddy and Lily to expose the dark secrets of the future, like how they are suppressing the lower classes or ruining the planet. So they would try to stop Teddy and Lily from going back to their own time with this knowledge.
Obviously, Harry and Teddy are the main characters. Harry is a well - known wizard from the original series, and Teddy is his godson.
The main villain could be a time - traveling version of one of his regular foes, like Slade. Maybe Slade from the future has developed a way to manipulate time and he's going back in time to stop Beast Boy from ever becoming a Titan or to change events in his past that will make him easier to defeat. Another option could be an ancient evil that was sealed away in the past and Beast Boy's time travel accidentally releases it. It then tries to take over the present by changing key events in history. And it could also be a future version of Beast Boy himself who has been corrupted by power and is trying to change the past to make himself even more powerful.
Kaguya Otsutsuki could also be a main villain. If Naruto travels to a different time period, he might accidentally release Kaguya or she could sense his Rinnegan power from afar and see him as a threat. She could then try to stop Naruto from changing the future or past in a way that would prevent her from being resurrected or stop her plans.
One idea could be Teddy time - traveling back to the time when Harry's parents were alive. He could try to prevent their deaths, which would create a whole new timeline. Harry would then have a very different life, perhaps growing up with his parents and without the burden of being 'the boy who lived'.
In most teddy harry potter fanfic, Teddy Lupin is at the center. But other characters like Hermione Granger could also play important roles. Maybe she helps Teddy with his studies or gives him advice. And Ron Weasley could be there too, adding some humor to Teddy's adventures. Also, characters from Teddy's family, like his grandmother Andromeda, might be included to show his family background and support system.