Snowfox - I sympathize. I really do. Mine is a multi-POV third person novel that follows a ton of different people around, and I've been having the same struggle (my most recent query edit I put up two versions focused on two different characters). The problem is that my most MC character is the one who is wrapped up in almost 100% mystery. What helped me, and what I would suggest for you, is to try writing the query following one MC, even if it leaves out some aspects of the story. Your only job here is to get the agents to read more, so a unified (albeit incomplete) hook is better than a scattered, whole one. If you need to, try writing a query for each MC, and see how it goes.
Jake Strickland is sixteen years old and has been dead seven times. Unknowingly, he has been hunted from birth for his one in a billion DNA This doesn't tell me what's so special about his DNA - I would suggest trying to specify. I assume, given the previous sentence, that it has something to do with his ability to come back to life, but that's not clear enough. And now, they have finally found him.
Secret Genetic Corporation, Artic X, has one mission: To clone an entire army of genetically gifted people like Jake and reprogram them into killing machines.
When Jake’s step-father, Hayden, goes missing at the Artic X laboratory, he He who? is nearly kidnapped when he goes to look for him there. He manages to escape with the help of his foster brother Luke and the Alliance: A group of teenagers sent to protect gifted people. Alright, I'm a bit lost. Why is said group of teenagers at the Artic (Arctic?) X lab... is he nearly kidnapped because the Artic (Arctic?) X people know how special Jake is?
The Alliance allow Jake and Luke refuge at their island headquarters, which is filled only with superhuman children and teenagers. Is Luke superhuman? I thought he was part of the Alliance, given the escape bit, but the fact that you say "and Luke" makes me think that he's a guest too
Here on the island and away from a society that never wanted them, the foster brothers are embraced into their new community, and build the family they never thought they’d have.
But when a traitor reveals the location of the island to Artic X, Jake and Luke know they must destroy the corporation, or they and their new friends will be cloned into a superhuman army of slaves.
YA light Sci-Fi, complete at 68,000 words. I assume you'll formulate this into a complete sentence when you're actually querying
You start out with great tension, but then it fizzles out. In my mind, this is reading too much like backstory, rather than the actual story, because all of the information about Jake being almost kidnapped and stuff has nothing to do with the ultimate stakes: he may lose his home/be cloned into a superhuman army. I would focus more about life on the island, since that's what will make us care about the fact that Jake is about to lose it. Great job focusing on Jake, though - I think he comes across as the MC without confusion.
Also, this is a minor thing, but what's with all the different font sizes? It would be best if you consolidate to one (although if it's tech issues, that may not be possible)