Meet my Hatchet of Death (or, some other colorful description RC Lewis and I come up with at any given moment). This is how I edit myself, it is how I edit others. If you think you want to play with me and my hatchet, shoot us an email.
We all know the first line of a query is your "hook." I call the last line the "sinker." You want it to punch them in the face, in a nice, friendly kind of way that makes them unable to forget you after having read the 300 other queries in their inbox.
If you're looking for query advice, but are slightly intimidated by my claws, blade, or just my rolling googly-eyes, check out the query critique boards over at AgentQueryConnect. This is where I got my start, with advice from people smarter than me. Don't be afraid to ask for help with the most critical first step of your writing journey - the query. My comments appear in green.
Just before her seventeenth birthday, when Lottie thinks that she’ll never figure out what her stress-induced synesthesia and the telepathic connection to a member of another planet called Karnock are really meant for, she meets a boy named Charlie. There's a LOT going on here, I'd say too much. For one thing, I have no idea what synesthesia is - and I'm guessing most agents won't either, so you're going to have to find a way to work an explanation into the query. Right now your hook sentence is too long and has way too many elements jammed into it. She doesn't sound all that alarmed about having this telepathic connection with an alien. He has similar powers as her, and he can maybe give Lottie the answers that she's been searching for. As they explore the truth behind their powers, they discover that it is up to them to save Earth from a malevolent enchantress that threatens utter destruction and slavery upon humankind. Technically, utter destruction and slavery are two different things. However, they also must save Karnock and its inhabitants, whose fate has been forever linked to Earth’s. This definitely needs explaining - why are their fates linked? And how do these kids actually feel about their powers, being the chosen ones, and each other?
Transported to Karnock, Lottie and Charlie see how the atomic bomb, Chernobyl, and global warming have all affected Karnock's population and landscape even more severely than they have affected Earth. How are they transported? What does this have to do with synesthesia and who is the alien she has a connection to?
Can Lottie figure out how Earth’s past ecological disasters fit into her current reality, gain control of her powers before she loses them completely why would she lose the completely?, and embrace her destiny on Karnock why does she have to embrace it? Is she resisting it? to defeat the enchantress, before the enchantress seizes power over both worlds? Definitely don't end a query with a question. I'm guessing that Lottie CAN in fact do all these things, or else it wouldn't be a very compelling story :)
I am currently seeking representation since you're querying, this is assumed for my completed that it's completely is also assumed 90,000 word YA science fiction/urban fantasy. Twice Affected is A Wrinkle in Time with a dash of An Inconvenient Truth. Either all caps or italicize your comp titles, and these sound like good choices.
I worked on this manuscript during the Fall 2013 semester at Simmons College with Amy Cherrix of Houghton Mifflin Harcourt as a project toward the completion of my Writing for Children Master of Fine Arts degree, which I received on May 9, 2014. Great bio here - you've done a good job of showing that you're serious about writing and have already made some connections.
Definitely work on getting this query boiled down to what's important - this sounds like SF with an environmental twist, which is pretty interesting. But right now there's so much information in your query that it's making the query look messy, and an agent will assume that the ms is messy too. Pare down what's necessary to whip the query into shape, and get your human elements into it - how do the kids feel about each other? About their destinies? Does Charlie even matter? He's mentioned once, but hardly seems necessary to the query, let alone the book. Boil down your book to it's most basic elements, then use those to reconstruct the query.