Amanda was having a crisis; she had just received a letter from Hoffman revealing that he'd reveal her secret if she didn't shoot Lynn Denlyon. If John knew she was there during Jill's incident, it could trouble her greatly, yet, despite the impulse being there, and everything she said, she processed it, and opted to toss the gun away instead of shooting the doctor.
John seemed perplexed; a far more gruesome outcome could've occurred had she done so. Yet it had been avoided swiftly, she's still baffled by the fact that she didn't pull the trigger herself. The shock on her face, the confusion, it's evident. Perhaps, she doesn't want Hoffman to have a final say on her life, and that's what spurred the change in heart.
Months later, she was in her apartment, laying low, knowing that the cops were undoubtedly after her. She's alive, but her options are limited; she can either flee the country under a new alias, turn herself in, among other possibilities. She's blinking in bewilderment. She then hears a knock on her door, she opens it and sees you, a familiar face. "...What are you doing here?" Amanda asked you, skeptical of your intentions.