I had this idea for a story I wrote about earlier. It is kind of like a comic book universe where it focuses on a few heroes at a time at a certain city or borough. I wanted the first 9 to have little if no connection between one another, and in the 10th to make a crossover of 3 books and repeat this. after the first crossover characters of other stories will appear. Basically, it's like comics but one book at a time. What is the best way to do it?
The first 9 what? Heroes? Books? If it's books, you're getting way ahead of yourself. Why are you planning your tenth book in the series when you haven't begun the first yet? I see this sort of thing here all the time - people talking about their plans for a ten or twelve book series. They're all selling their future selves short. You need to learn to trust your creative self. As you write, you will improve as a writer, and you will very, very likely come up with much better ideas than you have now. If you slavishly commit to following your original plan through, you'll be stifling your future, better self. You'll be forcing your best self to execute the plans of your worse self, so to speak. Just write your first book. If, when you're done, your current plan doesn't look kind of weak, you're not doing it right.
The first 9 story arcs, and it is quintessential for the series to be successful. I think now maybe they should comprise together an omnibus of short stories. Probably 1 main that 9 get out off and 1 int he end to conclude it.
So 1 story per character and a final one that includes several from the previous ones? I think it would be best if you were to write these characters in a series of short stories rather than giving each of them an entire book to themselves. I recall someone - Cogito probably - saying that rather than going straight into a series of books you should start small; mainly, you should begin doing simple things like short stories, and then progress into a standalone book, and then after that you might be able to look into writing a series. Making a ten book series is probably a bit of a stretch at that rate, though. After your standalone book you might make one or two more and then make a two book series, and slowly work your way up and get better and better and so on and so forth. Like Minstrel said, you should avoid committing yourself to a large series of books right now because later on you'll not want to change things about. This is somewhat similar to the idea of writing out the outline of a plot; if you write it all out before you actually go to write it then you might come up with new ideas that won't fit because you want to stick solidly to your plan. Sorry, I think I went on a little bit of a rant there. .
Another way you could do this is to have a single novel that combines all of your short stories - if the plots combine into a cohesive whole.