I'm sorry, I didn't read everything above, so I'll post here what I have in mind.
In my opinion, you don't need a theme to start a story. Just an idea, or a question ("what if mankind discovered and desided to make contact to a planet with intelligent life and [mankind] was treated as bad aliens? How would makind interpret and react to this?" for example).
Once you have the idea, you can start working on it. You can think about characters, scenery, things that happen, conflicts... although this may pop up on your mind just by thinking on the main idea (if it doesn't happen, don't worry, everyone's minds work differently). My suggestion here is for you to be sincere. Let the characters be themselves, let things flow. Would that character really do that? Would s/he really say that? Do people really speak this way? Would he say "damn, John!" or "fuck, John!"? Of course you'll want some things, some conflicts to happen so the reader can discover who that person actually is on the inside, but think of this as a fossil that you have to dig. The more you dig, the more you discover about this fossil. The idea is somewhere and your job is to bring it and put in on the paper. This is a tip from Stephen King that's on his book On Writing.
Note here: King's book is for writing novels. Writing for comics is different (and I'm honestly only starting to study and understand it), but I still think King's book is a good material, honestly.
Well, because writing for comics is different, I'd like to quote what Eagle recommended in this post.
I'd start with Scott McCloud's Understanding Comics and follow with one of those Writing for Comics or Will Eisner's Comics and Sequential Art. Then you can go on and study the rest of them. They really make a difference.
Well, sorry for the long post and I hope this helps you.