The Question and Answer section for A Wrinkle in Time is a great resource to ask questions, find answers, and discuss the novel.
Mrs. Which tells Meg that her father is behind the great darkness that they saw in the sky. Though Meg despairs at this fact, Mrs. Whatsit comforts her and tells her that they would not have brought her here if there was no hope.
Mrs. Murry means that just because we do not understand something does not mean it is true. There are more things in the universe that man does not understand compared to what he does understand.
Meg screams "father" trying to get past the man with the red eyes and appeal to her father if he exists somewhere inside the man with the red eyes.