It could be her best friend. In many stories, best friends have a special bond and can sense when something is wrong. So, her best friend might start looking for her and be the first to find her.
There's also a possibility that the father of the baby, if he has any feelings for Clary or the unborn child, might be the first to find her. He may feel guilty or responsible and go looking for her, eventually being the first to track her down.
Her mother is also a likely candidate. Mothers often have a strong intuition about their children. Even if Clary runs away, her mother might figure out where she has gone based on her knowledge of Clary's favorite places or people.
She may be running away to protect the baby. Maybe she fears that someone or something in her current environment poses a threat to the unborn child. It could also be that she wants to start anew, away from all the complications and expectations in her present life, so she decides to run away with the hope of building a better future for herself and her baby.
Sasuke could be one of the people to help. Despite their past differences, Sasuke has a deep connection with Naruto. He might be able to understand Naruto's situation and offer his protection and support.
The Weasley family could also be of great help. Molly Weasley, in particular, has a motherly instinct. She could take Harry in and help him with the pregnancy as if he were one of her own children. The Weasley twins might also be able to create some useful magical items for Harry to use during his time away, like special potions for a healthy pregnancy or charms to keep him hidden. And Ron, as Harry's best friend, would be there to support him emotionally and physically, even if he was initially shocked by the situation.
It could be Ron. Maybe they had a falling out or some sort of misunderstanding during their relationship, and Hermione runs away when she discovers she's pregnant. Another possibility is that it's a new character, someone she met during one of her adventures or studies. This new character could be from a different magical culture, and their relationship was a secret.
She could meet other outcasts from the wizarding world. There might be witches and wizards who have left Hogwarts for similar reasons and they form a sort of community in hiding. Maybe she'll meet a powerful but reclusive wizard who can teach her things that Hogwarts never could.
One possible scenario in this kind of fanfiction could be that Ginny discovers she's pregnant at a very inconvenient time. For example, there might be some dark forces rising again in the wizarding world, and she fears for the safety of her child. So she decides to run away to a secluded place, perhaps a small cottage in the countryside that she discovers through some old family connections. This would also give the author a chance to explore Ginny's maternal instincts and her ability to fend for herself.
He could meet some of Iwa's powerful ninjas. Maybe Onoki, who could either see him as a threat or an opportunity. There might also be some young Iwa ninjas who are curious about Naruto and his abilities.
He might meet some of his distant Uzumaki relatives. There could be elders or other Uzumaki clan members who have valuable knowledge about his family and their special abilities.
A kind stranger could come to his aid. Maybe someone who has been through a similar situation in the past. This person could offer practical advice on how to survive while being on the run and pregnant. They might also teach Stiles some skills like cooking healthy meals for the baby's sake.
Perhaps it's an enemy character who she had an unexpected encounter with, and this led to the pregnancy. It would add a lot of drama to the fanfiction as she then has to deal with not only the pregnancy but also the implications of the father being an enemy.