I am overstayed my F1 visa and was planning to leave. But now I want to marry a citizen and either take her back to Japan or stay here. If we do get married can I get legalized and green card or must we both leave?

Please help me as I am at wits end.

Get a lawyer! You have already broken the law and overstayed your visa. You need professional help. Your worst case scenario now is that you get kicked out of the country with your wife. I assume you don't want that.