You are able in some instances to give characters, major and minor, grit, distinct personality traits, voices and thought patterns. But sometimes you over-describe your characters physically, yet, as I wrote above, have them (Mr. X, for example) act in ways incommensurate with the abilities and backgrounds you’ve initially given them.
While you may want to give the impression that they’re somehow rising to heroism, you have to plant seeds for their deeds, so to speak. X seems to be the nearest character you’ve created to a protagonist, but he just doesn’t seem “big” enough to cut the muster.
Perhaps for this reason, you leave much of the resolution of the plot to hosts of minor functionaries in fact, the magnetic pulse itself is stopped, not by X (though he does expose a key fraud), but by a relatively inconsequential person.
(As I’ll explain later, if you have a positive protagonist, he or she should be the direct instrument to bring down the antagonist, or villain.) So in a sense your story gives the impression of boiling down to Y and a couple of his cohorts (cf. Z) vs. a host of Lilliputians. Since even collectively Y’s opponents don’t seem a strong enough force to bring him down, I’m going to suggest a radical shift in the book’s focus:
Make Y himself the book’s focal point and main character.
This suggestion may at first seem strange and even deleterious to your scheme, because much of your narrative’s occupied with X and other characters solving the plot’s main “jigsaw puzzle,” piecing together the mystery and eventually working to bring Y down. Problem is, all this is done in such a scattered manner that it doesn’t really add up to more than the sum of its parts. This way of doing things doesn’t allow a single, sufficiently strong protagonist to develop to make their collective ability to dismantle Y’s scheme credible.
It’s true that generally a good fiction plot needs to build on a working structure that’s seldom found in ideal form in short or long fiction, a sort of “skeleton” having five major “bone structures”:
1. A believable and sympathetic central character;
2. Her/his urgent and difficult problem;
3. This central character’s attempts to resolve the problem, which all not only fail, but make his/her situation ever more desperate;
4. The crisis character’s last chance to win;
5. The plot’s successful resolution, brought about by actions directly springing from the central character’s own strongest character traits: courage, ingenuity, intelligence, passionate love, sense of duty, etc.
To fully engage readers with a narrative it’s crucial that they have this one character with whom they can identify and for whom they can root. In X’s case, he doesn’t have from the start a particular problem on which the novel hangs. By and by he discovers he has one, but this doesn’t grab us quickly or strongly enough, nor do the issues of any other character in the novel but one: Y, who has designs to take over the world. His problem? How’s he going to do it?
How can Y possibly become the novel’s central figure? By employment of the reverse of the above plot structure by creation of a story in which the villain is the central character, whose problem involves attempting successful perpetration of his/her villainy, and whose story ends, rather than with his/her victory, with his/her defeat, “sowed” and eventually reaped as a result of flaws, oversights or (sometimes) overweening over-confidence or misjudgment in his/her very character traits that have almost enabled him/her to “get away with it.” (I’ll e-mail you a copy of an evaluation of a successful book written in this sort of paradigm, to give you a clear idea of how this type of structure works.)
In other words, from the very beginning, instead of being left in the dark about Y’s designs, the reader’s let in on them he also seems to possess overwhelming power and resources to fulfill his schemes. Y’s designs are painted in such stark and horrifying terms that, in a mirror image of a sympathetic character, readers are enraged and frightened enough to root against him from the get-go, and the story’s suspense is generated by the issue: How in the world can he possibly be brought down?
Yes, if you take this tack you do sacrifice the “mystery”/jigsaw puzzle X and others assemble. But I don’t think it’s much of a loss, especially since with the disjointed way you’ve written the positive actors’ characters and their actions, true suspense and mystery never really develop.
I think deeper suspense and mystery can be developed as readers come to sense through Y’s eyes and growing fears that he suspects someone’s catching on to him and satisfying resolution can come as he gets his comeuppance. X can still lead the way, as Y’s positive antagonist, but I think moving in this direction will make both the collective impact of the “Lilliputuans” and Y’s bring-down from internal character-causes more interesting and believable.
Let’s move on to an area of narrative difficulty your novel has, managing your handling of your many characters’ points of view.
Part 1: Introduction and Overall Assessment
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