Alrighty, by reading the title, you can probably tell what this is all about.
Here's a list of questions you should answer before starting out with a story of your own:
- Do you like it enough to stick with it?
- Is there a moral at the end of your story?
- What will be the point of view?
- What is the conflict? Will it keep the reader hooked (is it intruging?)
The first thing you need to keep in mind before making a story, whether it be for a manga or for a book: Do you like it enough to stick with it? If you can't say you do, you'll never get anything done. Try to think of something that you ABSOLUTELY LOVE, whether that is dragons or other fantasy creatures, magic, school stories, making people laugh (comedies), adventures, mysteries, 
romance
, anything at all. Go ahead, even make a character out of a purple dinosaur. Put yourself in the characters' shoes; maybe then you might get into it a bit more.
Next: Is there a moral at the end? Alot of people write to teach other people something, or get an idea into there heads about something else, or help them understand a feeling or whatever. Not every story has a moral, but they can make a book more interesting (this isn't usually used in mangas). Even if the reader doesn't learn anything, maybe a character in the story itself will learn it.
Do you know your point of view? Are you looking from just the main character's perspective? Are you omnipresent, or viewing several things at different times?
Or just simply looking through the main character's mind, only showing the main characters thoughts? This can make or break a good story. Omnipresent views can give away too much information too early, spoiling everything else unless you're extra careful. Some authors switch the point of view from chapter to chapter, looking through a different character's eyes each time, getting a different look at the story, usually picking up where the last character left off, or a bit before. In a manga, you can simply show only one person's thoughts through one chapter, then anothers in the next. Or you could just show any and all (make sure the readers can tell who's thinking what, though--it can be a disaster if you don't make it clear enough!)
Another thing you need to remember: if your plot is boring, your conflict dull, your work will loose its quality. So what if the characters are funny and/or adventurous? If there isn't a conflict, it'll just go downhill. Make the character(s) take a trip to the moon. How will they get back? Are they searching for something? Is someone trying to win someone's heart? Is the character trying to get over an old pain, an old fear? Do they have to defeat one person or another? Is there a mystery to solve? Once you know the conflict, all it takes is a little creative brainstorming to come up with how it comes to be! Or maybe it doesn't! That's how sequals come to be...!
Of course, there are many other questions one should ask themself when creating a story, but these are the first few. Remember, these are important, so keep them in mind! They are the stepping stones to becoming a good writer, or good mangaka, or whatever you're shooting for!
And finally, the second animusic on the sight! (see the welcome post for the first!
