A Wrinkle in Time by Madeline L'Engle (1963). Actually, when we picked this one, none of us were really sure how much of a downer it even was (although it did show up on some "sad young adult books" lists). I'm not sure how, but I somehow avoided reading this book for my entire childhood, even though I have been reading pretty much constantly (with short breaks for eating, sleeping, and working) since I was 4, and this book would have been right up my alley!
Never fear, guys, it does have some solid downer content, including: missing father, bullies, scary physics-involved space travel, realization that adults can't save or protect you, isolation and loneliness, potential loss of favorite sibling, etc. And things don't really wrap up happily until the last three pages!
In case you are a weirdo like me who never read this one before, the basic outline is that Meg's father, a scientist for the government, disappeared mysteriously. She is teased at school because of her father and her temper is a little out of control. Her brother, Charles Wallace, was a baby when their father vanished. He is five going on twenty-five with some unusual psychic abilities. They, together with Calvin O'Keefe, a popular kid from school who has some of the same psychic connections as Charles Wallace, are whisked away by the very unusual Mrs. Whatsit (and soon joined by her colleagues, Mrs. Who and Mrs. Which) and set out on the adventure of finding Meg's father and saving the world from evil / darkness / the cloud / IT.
There is some solid sci-fi in here, as well as a good dose of Christianity (which I totally would not have noticed as a kid) and some pro-American / anti-communist mindsets. I was particularly into a nice little homage to Flatland, one of my favorite mathematically-based science-fiction books. The characters are types, but they are lovable types, and there is a lot to enjoy in Meg's journey towards independence and (of course!) the power of love. This is the first book in a short series, and I'm down for checking out the rest.
Finally, thanks to my book club, I did discover the existence of this really horrible and extremely dated 2003 film version of the book that features possibly the weirdest line delivery, most awkward special effects, and downright creepiest Charles Wallace ever.