It could be a jealous wizard who was once in love with Hermione. Discovering she has a child with Fred, this wizard might seek to harm the child out of spite. He could use dark magic to try and kidnap the child or cause trouble for the family.
One idea could be that the child has unique magical abilities that neither Fred nor Hermione expected. Maybe the child can communicate with magical creatures in a way no one else can. Another plot could be the secrecy around the child's existence causing all sorts of misunderstandings among the Weasley family and Hermione's friends. For example, they might suspect Hermione of being involved in some dark magic when they notice her acting strangely to protect the secret.
Perhaps a powerful magical being from a different realm is the antagonist. This being might mistake Hermione for someone else or see her as a key to something in the wizarding world. So, it uses its magic to make her disappear. This being would be very difficult to defeat or negotiate with, making it a huge challenge for those trying to find Hermione.
In fanfiction, a Fred and Hermione secret relationship often adds an interesting twist. Writers might explore how their different personalities interact. Fred's humor and mischievous nature could contrast with Hermione's studious and rule - following side. It could start with a chance encounter in the Hogwarts corridors, leading to shared secrets and a growing bond that they keep hidden from their friends for various reasons, like fear of judgment or disrupting the group dynamic.
Perhaps the child is on a quest to bring back a lost magic that was present in the past but will be crucial for the future. Fred and Hermione are initially skeptical but as they see the child's abilities and the evidence of the disappearing magic, they start to believe. Together, they embark on a journey to find ancient spells and artifacts that can restore the magic, all while dealing with the challenges of time travel and the secrets the child holds.
Dr. Eggman would be a likely choice as he often causes trouble for Sonic. In the context of Secret Wars, he could have found a way to connect Sonic's world to other dimensions and start the wars to finally defeat Sonic once and for all. He might be using new and powerful machines he has created from the combined technology of different dimensions.
It could be a rogue ANBU member who has gone bad and is trying to expose Naruto's secret identity for some evil purpose.
A powerful sorcerer who wants to harness the power of the earth and sky for his own selfish gains could be a great antagonist. He might try to corrupt the natural balance to gain unlimited power.
Another possibility is Harry Potter himself. This would be a very different take on their relationship. In some fanfiction, the strong bond between Hermione and Harry could be taken to a new level. Maybe in a situation where they are the last hope for the wizarding world, they conceive a child in secret to carry on some special magic or power that could save the wizarding community.
It could be the same group or person who tortured her in the first place. They might be trying to finish the job or silence her before she can expose their evil deeds.
Hades would be a likely main antagonist. He rules the Underworld and might see Hermione as a threat or an opportunity. If he thinks she has something valuable, like her knowledge of magic, he could try to keep her trapped in the Underworld. Or he might oppose her if she's trying to change something in his domain that he doesn't want changed.