Survival
In the opening of this book, we learn not to feel bad for Ellie. Even though she is only 12, she is competent. She avoids capture by Mal. When captured, she fends well for herself. She escapes his pursuit in her space pod, and in the ending of the novel, we see that she has only grown in her survival skills. She is competent enough now to care not only for herself, but also for her kid brother who depends on her for his own survival.
Evil and power
Evil is depicted in the character Mal Gorman, whose first name is literally Latin for "bad," who kidnaps Ellie and lies to her family that she died. Why? Because as a young person in crisis, Ellie has developed psychic abilities that Gorman wants to exploit. He is evil because he uses his power to exploit the weak and helpless, to get more power for himself. He opposes the good forces of family and nature.
Nature and humanity
What is a human if not an animal? Yet, this novel alleges that humans killed all the other kinds of life on earth with toxic yellow gases. Meanwhile, Ellie desires the state of nature deeply. For instance, the novel opens with her literally returning to earth, and it ends with her returning to earth in another way. The first time, she is returning from capture and captivity, and from abuse. The second time, she is departing civilization to go back to her true habitat: earth's wilderness.
