Stories in manga comics typically are serialized, usually in magazines. When you brainstorm for a story idea, consider a tale that can be told over several "issues" or "chapters." Imagine the story will be published in chapters no more than four pages long, and build your idea on this format. Build a story arc that can be told in 10 or so chapters, or 40 pages. Create individual story arcs that propel the larger story for each of the four-page chapters.
Manga comics are separated by age. There are manga for young children and teens, and manga for adults. Manga sometimes is separated by gender, with stories that attract men and women individually. Tailor your story to the audience you prefer. The subject matter might be the same, but the treatment, or the maturity level, dictates how the story is told.
When you create your story, focus much of your attention on the main character. Western comics such as "Green Lantern" and "Superman" often are dominated by plot and action. Character usually comes second or even third to a high concept plot about a supervillian seeking world domination. Most manga writers, on the other hand, delve deep in a character's past and explore what makes him tick.
In recent years, manga tradition has focused on cinematic thinking, or telling stories in a visual style similar to film. When you brainstorm your characters and story, consider how those elements would appear on the silver screen. Use those images to inform your art and how the story unfolds.
Modern manga comics tackle any subject you may imagine, from joke books to historical novels. By comparison, Western comics are dominated by superheroes and blockbuster action. So if your tale is one about lost love or exploring the rain forest, there's a place to tell that story in manga.