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Kilroy’s a rowdy junkie living out of his car and Mary’s a stoic widow with a sword. A literal one? It's not mentioned again so I'm confused on this point. They were never designed to like each other. I think you can kill the line before this. After finding Mary’s husband overdosed in an alley, Kilroy’s life becomes violently chaotic as they both end up searching for the same dealer: the Funnyman. Kilroy’s looking for his next fix while Mary’s more interested in revenge. The pair can’t seem to avoid each other, despite their mutual contempt. Are they teamed up, or just running into each other occasionally?
After Mary kills the Funnyman’s goons, he mistakenly blames Kilroy and holds him prisoner in an asylum. When Mary discovers Kilroy’s been accused and tortured for her crimes, she feels guilty and tries rescuing him. Despite rescuing Kilroy and bonding over similar goals, Mary realizes the Funnyman’s fled. He might’ve been able to elude them when divided, but the dealer’s never experienced their combined wrath. Piling into Kilroy’s car, the pair drives out to confront the Funnyman one last time. Drives out to where? Right now this is reading like a synopsis, not a query.
Kilroy doesn’t realize Mary enjoys the killing, but Mary has no idea Kilroy’s still just looking for another fix. So they are deceiving each other, to some extent. They hope their lies can survive till this one job’s over. Why? How important is it that they like each other, when they have a shared goal? But the Funnyman’s too clever; he sees both of their inner desires, and he’s just itching to expose them at the worst possible moment.
NEON (112,000 words) is an offbeat cyberpunk story set in a futuristic version of the 1990s. Mary and Kilroy might hate each other, but they’ll have to work together to stand a chance at finding the Funnyman.
You wander too far into synopsizing in the second para. The agent doesn't need the details in the query, just the feel - which you do have, mostly. Biggest question for me is, to what extent does this relationship go? Are they the "odd duo" that ends up together? Is there an attraction? Or is this just "lets put up with each other for now, then we're quits." That needs clarified.
Also, how important is it that they get along? It sounds like the Funnyman is going to reveal their weaknesses, each to the other, but why does that matter? If they really don't like each other, how is that a threat? Lastly, (and this may seem simplistic) but why can't Kilroy just get his next fix somewhere else? Surely the Funnyman isn't the only dealer around.
And - why is he called the Funnyman? It's an odd moniker for a drug dealer. Is he a practical joker? Flesh him out a little bit more and get the relationship between Kilroy and Mary clarified a bit more, since it's the meat of the story.