Perhaps there is a dark force that is awakened by the oc's reincarnation. This force might have been dormant for a long time, and the oc's new life energy or something about their reincarnation stirs it. It could be a force that wants to destroy the balance of the pjs world, and the oc is the only one who can stop it because of their unique perspective from their past life.
One idea could be that the oc retains some memories of their past life. So they use their knowledge to change things in the pjs world. For example, they might know of a coming danger and work to prevent it.
Maybe there is a new character created specifically for this fanfiction as the main antagonist. This new character could have a connection to the oc's past life or the reason for their rebirth. They might be trying to prevent the oc from fulfilling a certain destiny or unlocking their full potential.
It could be another powerful ninja who sees the student as a threat to their own power or plans. Maybe someone who doesn't want Madara to pass on his knowledge to an outsider or a young upstart.
An ancient and powerful entity that has awakened from a long slumber. It could be some sort of dark psionic being that wants to consume all life in the galaxy, starting with the Protoss and the OC's army.
Another possibility could be an original antagonist created specifically for the fanfiction. For example, a powerful sorcerer from a hidden dimension who sees the OC's rebirth as a disruption to the natural order of the MCU universe. This sorcerer could try to eliminate the OC and use their power for their own dark purposes. They might be able to manipulate magic in ways that even Doctor Strange hasn't seen before, making them a formidable foe.
Perhaps another reborn character could be the main antagonist. Say, an evil sorcerer from the past who was also reborn in the Inuyasha world at the same time as the OC. This sorcerer has his own agenda of ruling the world and sees the OC as a threat to his plans, especially if the OC is getting in the way of his attempts to gather the Shikon Jewel fragments.
It could be another powerful character who is jealous of the growing relationship between Copperhead and the male OC. This character might see the male OC as a threat to their own power or influence over Copperhead. For example, if Copperhead is a leader in a certain group, this antagonist could be a rival within the group who wants to undermine Copperhead by getting rid of the male OC.
Another possibility is an old enemy of Klaus. They might see this situation as an opportunity to get revenge on Klaus. They could try to use the OC's pregnancy to manipulate Klaus or cause trouble between him and the OC.
Lex Luthor could be a main antagonist. If the oc is trying to promote a new form of clean energy or something positive in Metropolis, Lex would see them as a threat to his own power and business interests. He'd use his intelligence and resources to try and stop the oc.
It could be an ancient evil entity that has been sealed away for centuries. The OC's rebirth somehow disturbs the seal, and this entity awakens. It views the Fairy Tail guild as a threat because of their positive influence in the world. So, it starts to target the guild, and especially the OC, as they are a new and unknown factor in the fight against it.