L'Engle touches on difficult themes: trust, avocation/vocation, science and ethics, good vs. evil, thinking on the consequences of your actions, and of course it wouldn't be L'Engle if love didn't tie these all together.
L'Engle gives many clues to who is good and who is evil in the book (particularly names: Kali, Typhon, Eliphaz Ball - initially pronounced "Baal", Molec), but writes so well that the confusion Adam (the main character) is feeling is felt by the reader as well. Even many of the good guys have names that indicate their righteousness: Joshua, Archangelo, "Old Doc" Didymus. There is a fight for good & evil over Adam's soul and to help him see how to be ethical in his chosen vocation.
Vocation is a big theme here, and not just vocation, but being called to work you love and loving the work you do. This theme is brought clear through L'Engle's use of Robert Frost's poem Two Tramps in Mud Time.
(If you only follow one link from this post, follow that one, the poem is so full of meaning).
Ethics is the final theme I want to discuss. Dr. O'Keefe (Adam's employer) is working on experiments that could easily go wrong; especially if used on humans. Typon Cutter wants to use Dr. O'Keefe's work for his own fiscal gain. Dr. O'Keefe, talking to Adam:
We're just beginning to learn why the regeneration [of starfish arms] is sometimes abnormal and malignant. We're just beginning to understand that you cannot change stones into bread. This is not the way miracles are worked, but it's always been a temptation. If what we are doing is taken over by the unscrupulous it can cause unimaginable horror and suffering. Here is power to give life to people, or to devour them. What I am trying to do is to go back about two thousand years in my thinking. Somewhere in the last two thousand years we've gone off. When we began to depend on and to develop things in the western world we lost something of inestimable value in our understanding. There's something wrong about trying to heal with a surgeon's knive. There's got to be an alternative to cutting and mutilating and I'm trying to learn it from the starfish. But I'm just at the beginning. And I'm afraid, Adam. If it gets out of my hands--I'm afraid.(bold mine, italic L'Engle's)
There is a lot more to this book; self-sacrifice, love of neighbor, how to be a good friend, but you'll have to read it for yourself to see it all. This book, of all of L'Engles, can stand alone, although characters show up in her other works as well. It is a book that will make you think.