One mysterious boy name could be 'Elias'. It has an old - world charm and a sense of mystery. Another is 'Orion', which is associated with the constellation and gives a feeling of being otherworldly. 'Caspian' is also a great choice as it brings to mind the vast and mysterious Caspian Sea.
Consider 'Kieran'. It has a Celtic origin and a sense of mystery. It can be a name for a boy in a story who has a connection to ancient magic or a forgotten lore. 'Onyx' is another mysterious name. Just like the black gemstone, it implies something dark and precious, a character who is rare and full of secrets. 'Jet' is also a good choice. It has a sleek and mysterious feel, like a character who is fast and elusive.
Ophelia is a very mysterious name. In Shakespeare's play, Ophelia is a complex and somewhat mysterious character. Another option is Lyra. It makes one think of the constellation, something far away and full of mystery. And there's also the name Iris. In Greek mythology, Iris was the goddess of the rainbow, which can have an air of mystery as it bridges different elements and is often seen as something beautiful yet not fully understood.
Cypher. The word 'cypher' itself has connotations of secrecy and mystery, as it is often associated with codes and hidden meanings. A character named Cypher in a story could be a master of secrets, perhaps a spy or an expert in decrypting ancient texts, his true identity and motives always kept under wraps.
Natalie. It has a certain elegance and mystery. Natalie could be a character who seems ordinary on the surface but has a double life. She might be a spy or an artist who creates works that are full of hidden meanings. Her true identity and intentions are veiled, making her a mysterious figure in the story.
For a story, you might consider the name Ethan. It's modern and has a friendly sound. Jacob is also a great choice as it's been quite popular in recent years. Then there's Benjamin, a name that can be associated with intelligence and kindness.
Avalon. It has strong associations with magic and mystery in Arthurian legends. Another name is Morgana, which is often depicted as a powerful and mysterious sorceress in those same legends. And Nimue, also known as the Lady of the Lake, is a very mysterious and magical name for a girl in a story.