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I didn't see or know much about why things happened in Linger, but after thinking back to what I read, I realized what the whole novel was containing.
It was all about running away from your problems. On Sam's part, it was about maintaining human and staying in his life. For Grace, it's about keeping her health problems away because she is afraid of what might be happening to her body. For newbie, Cole, it's about running away from a life of emptiness and from being himself. It's all about the characters learning the courage to face their problems before their phase in the third book. That is my opinion, anyway.