Brian Falkner's The Tomorrow Code is chilling YA sci-fi. The first time I read this book I remember staying up late to finish it because if I tried to sleep without reading the end, I knew I would be plagued with nightmares. This is a book with an agenda; the message of ecology and human meddling isn't hidden. However, the story is told well enough that this is actually very effective instead of being preachy.
Tane and Rebecca are two New Zealand teenagers who are both intellectually gifted. When Tane comes up with a hypothetical way to listen for messages sent from the future, Rebecca realizes it, and the two are shocked to find that such messages do exist - and their contents are chilling. Now the two of them, with Tane's brother, must figure out how to prevent the disaster to which the messages cryptically allude. Throw in some well-written YA relationship drama along with the science, and add a dash of post-apocalyptic horror, and you've got this book.