The main antagonist could be an old, corrupt house - elf. This house - elf was mistreated in the past at Hogwarts and has now turned to the dark side. It wants to bring chaos to Hogwarts and sees Lady Hogwarts as the key. It uses its knowledge of the school's hidden passages and secrets to plot against her. Harry Potter, being the defender of the underdog, tries to reason with the house - elf at first but when that fails, he has to use magic to stop it from harming Lady Hogwarts.
It could be a dark wizard who has infiltrated Hogwarts' staff. This wizard might be secretly manipulating events and students for his own dark purposes. He could be using his position to spread dark magic teachings and trying to turn students against each other, all while Lily Luna Potter starts to suspect something is wrong and tries to expose him.
The main antagonist could be an ancient evil spirit that has been awakened by the mixing of ninja and wizarding magic. This spirit is angry at the intrusion and starts to possess students and teachers at Hogwarts. The ninja and Harry Potter must figure out how to exorcise the spirit before it's too late and Hogwarts is completely taken over.
It could still be Voldemort. Even though the focus is on Harry and Nagini, Voldemort is Nagini's master and the main source of evil in the Harry Potter world. He would likely try to stop Harry from getting too close to Nagini or from finding out any secrets Nagini might hold.
It could be a dark wizard who is jealous of the bond between Harry and Lily. This wizard might try to break their connection and use Lily's power for his own evil purposes. Maybe he wants to control Lily's magic, which is known to be strong, to achieve domination over the wizarding world.
It could be Voldemort who somehow follows Harry into the realm of the Morrigan. His dark magic could disrupt the balance there and make him a common enemy for both Harry and the Morrigan.
There could be a group of anti - magic fanatics in the fanfiction. They see Byako as an abomination because of his strange powers that don't conform to the normal rules of wizarding magic. They also view the Hogwarts students' acceptance of Byako as a sign of the corruption of magic. So they set out to eliminate Byako and anyone who stands in their way.
A dark wizard or witch from outside Hogwarts could be the main antagonist. They might target Harry specifically because of his reputation as the 'Chosen One' and use their influence to get him expelled from Hogwarts so that he is more vulnerable and easier to attack.
One possible plot could be that Lady Hogwarts is a long - lost magical being who has been dormant for centuries. Harry Potter discovers her during one of his adventures in the Forbidden Forest. She has the power to manipulate the very essence of Hogwarts itself. Harry, with his inquisitive nature, tries to learn from her about the ancient magic that she holds, and together they face a new dark threat that is emerging from the shadows of the school's past.
It could be the person who sent the venomous snake after Harry Potter. Maybe a dark wizard who wants to harm Harry.
There might be a new character introduced in the fanfiction who is using the appearance of the Grim Reaper to cause chaos. This character could be a dark wizard who has found a way to mimic the Grim Reaper's powers and uses it to spread fear among the wizarding community. Harry would then have to figure out who this impostor is and stop their evil deeds.