There might be a group of people who believe that Sev is dangerous because of his potential power. So they are trying to eliminate him. Lilly has to convince them otherwise or stop them from harming Sev.
Well, perhaps Lilly realizes that Sev is in some sort of danger in the past that leads to a tragic end in the future. So she uses a magical device or spell to travel back in time. Once there, she has to find Sev among all the chaos and danger. Maybe she has to disguise herself to fit into the time period. Then she'd try to prevent the event that would have doomed Sev.
One possible plot twist could be that when Lily goes back, she discovers that saving Sev is far more complicated than she thought. Maybe there are forces in the past that are determined to keep the original timeline intact. Another twist could be that in her attempt to save Sev, she accidentally changes something else in the wizarding world for the worse.
It could be a dark wizard that was previously unknown. Maybe this wizard has a grudge against Harry's family for some long - forgotten reason and is using a very subtle and complex plan to harm Harry. And Fred discovers this wizard's plot when he goes back in time.
It could be a time - traveling version of Orochimaru. He might have his own plans for the past and Sasuke's interference could put them at risk. So, he tries to stop Sasuke from changing the past in a way that would undermine his future goals.
It could be Danzo. In the original story, Danzo was a major factor in the Uchiha massacre. If Itachi goes back in time, Danzo would likely still be plotting against the Uchiha. His thirst for power and his extreme methods would put him at odds with Itachi's new attempts to save the clan.
It could be Zeref. If Natsu goes back in time, Zeref might have different plans or be in a more powerful position at that time. He could be the main obstacle for Natsu to overcome, especially if Natsu is trying to change things related to the dark magic that Zeref wields.
It could be a time - traveling version of one of his existing villains. For example, Zoom could have found a way to travel back in time and is trying to change history to make his own future more powerful. Another option is that a new character, a time - keeper type of villain, emerges. This villain's goal is to stop Barry from messing with the timeline and will do anything to preserve the original course of history, even if it means harming Barry.
It could be a powerful sorcerer from the time she travels back to. This sorcerer might sense that Elena doesn't belong in that time and wants to stop her from interfering with his plans. Maybe he has some dark magic he wants to use to take over the kingdom or town she's in.
Perhaps an ancient martial arts master who has gone astray. He might envy Kenichi's pure heart for martial arts and tries to corrupt him. This antagonist could use his deep knowledge of ancient martial arts against Kenichi, creating intense battles between them. Also, he might try to use Kenichi to gain more power in his own time period.
Maybe the main antagonist could be an older version of Madara Uchiha who has somehow found a way to manipulate time as well. He might be trying to change the past in a way that benefits him and his grand plan for the ninja world, which would put him in direct conflict with Jiraiya.