Writing a query is hard. Mm-hmm.
Why is an eccentric genius [Seems like there are a lot of geniuses who are eccentric. What other unique traits has Foster got going for him that you could mention? What's his occupation, or something like that?] like Foster locked away in a psychiatric prison in PA? [I wouldn't begin with a question. It's everyone's first instinct (mine too), but it seldom plays well. Tell us what the situation is.] Because he discovered a signal from outer space. Then, he ignored the head of the NSA by obsessively pursuing the signal’s meaning. But, it wasn’t until he began screaming “Little Green Men” that national security was ever brought up.
Years later, the signal occurs again. Only this time, the problem isn’t theoretical. People are dying. And with time slipping away, Foster’s intimate knowledge suddenly makes him invaluable. [These two paragraphs could probably be condensed into a nice hook. Yes, it's interesting that he heard a signal from space and was arrested. But it's even more interesting that the signal recurred. Seems like a hook there.]
Desperate for answers, the person who placed him in prison dispatches Justine. Shoot first and ask question later, the FBI agent and her partner’s orders are very clear: keep an eye on Foster, discover the truth behind the signal, and stop anyone else from dying.
During their investigation, Justine and Foster butt heads constantly [If you mention this at all, be specific. What do they butt heads about ? What sort of consequences are there that figure into the story? Does it prevent them from cracking the mystery?].
Each confronting the same problem but with very different goals. Foster looking for the cause. While Justine simply wants to save people. Along the way, others join the team for assorted reasons. Each with their own special set of skills. Each shedding light on how immense their problem really is. [You don't need this, especially if you're not telling us what these "reasons" are. Keep the focus on Foster.]
But everything changes when an unassuming deputy comes forward. A person whose confessions lead them beyond the stratosphere to explore fantastical ideas like beaming technology, rickety spaceships, and alien arbiters. [Do they go up into space?]
More surprising: The deputy claims the earth is nothing more than a prison. One so remote, that only the worst criminals in the universe are sent there. [Ah! Now THAT's interesting! You would know better than me, but this sounds like the heart of your story. Guy hears a mysterious signal from space. He's alternately persecuted and consulted about it. Signal shows that Earth itself isn't what it seems. If I've got this right, that's what your query should be about.]
Satisfied, Foster takes his answers and resigns himself to move on [Wait. What? Earth is just a prison and Foster is okay with this? Where's the final conflict/showdown/race to the truth? I'm sure it's in your novel, but it's not coming through here. That's got to come out. You've got an interesting premise. What are the specific consequences of finding out the truth?]. To look past the years in prison toward a life before the signal. However, Justine’s unrelenting need to protect the innocent proves too much for him to ignore. Eventually, he’s swept away by her conviction on a journey to save the planet from an invasion no one knew was happening.
Broken Marvels (125,000 words) is a science fiction adventure/mystery.
As I said above, I like the story idea and premise. But (as others have said), the main thread of the story is getting lost in this. I've made a guess at what the story is, but you know best what you were trying to do in the novel. Bring that out in the query. Foster discovered all this groovy stuff (alien signals, Earth not being what it seems). Okay, now what? What does he do about it? What happens now that he's discovered all this. That's got to come through in the query.
Also, give much thought to specifics. Phrases like 'everything changes,' and 'swept away by her conviction' don't tell us (or show us) what's actually happening. WHAT happens? WHAT effects does it have on the story? That's what has to come out in a query. (I get where these vague phrases come from, because I've used a few of them myself. Queries have to be short. 'Everything changes' is two words. Describing what actually happens takes up many more words. But if those many more words better convey your story, then you're doing the right thing.)
Finally, focus on Foster as much as is practicable. In a 125,000 word novel, I'm sure a lot of things happen, there are many characters and more than a few interesting subplots. You can't talk about most of that in a 300-ish word query. What's the overall point of the novel? What does Foster do that's most important to the story's main purpose? How do his actions succeed (or fail) in bringing about a solution to the story's most significant conflict?
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