" When a Muslim is going to do something ; if it is halal his heart will agree with it; if it is haram the heart will be in doubt "
I believe it might be okay if you write your comic. If it portrays Islam in a good tone then it is permissable. If it might help others to get to know more about Islam then it is OK. The story is OK as long as it doesn't adversely affect your Iman. If it will make your readers forget Allah ( and what not ) , then it's not OK.
However if you portray terrorism and violence ( especially on the hero's part ), then you might have a problem. Islam is a religion of PEACE and if it promotes that ideology it's OK.
However at the same time you must not insult other religions in any manner. Because I believe you will make it available to everyone. Islam does not ask you to insult others :|
It is best to first give a sample of the story to a close friend or family member and ask them for their opinion ( what they feel about the story ).
Allah knows best.