Perhaps Voldemort himself could still be the main antagonist even in this fanfiction scenario. He might find out about Harry's encounter with Lily and see it as a threat to his plans. So, he would do everything he could to stop their collaboration and destroy both Harry and Lily once and for all.
Another option for the main antagonist could be a group of pure - blood supremacists who oppose Lily because she is a Muggle - born. They might see Harry's interaction with her as a sign of him going against the so - called 'pure - blood values' and try to get rid of both of them to maintain their ideas of a 'pure' wizarding society.
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 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.
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 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.
It could be a dark wizard who wants to prevent Ginny from meeting James and Lily. Maybe this wizard has some grudge against the Potter family and knows that if Ginny meets them and learns something important, it will foil his evil plans.
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.
Maybe it's a group of dark wizards who believe in a more extreme form of pure - blood ideology. They see Arcturus Black as a traitor for teaming up with Harry Potter, who is a half - blood. They plot to take over the wizarding world and eliminate anyone who doesn't fit their idea of a pure - blood wizard.
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 Bellatrix Lestrange. Since she is a Death Eater and has a personal vendetta against Sirius, she would be a great antagonist. She might try to kill Sirius again and also target Harry to please Voldemort.