 In the prime universe , Nina Sharp helps to set up Massive Dynamic 's resources to track these occurrences , preparing to deploy limited supplies of the amber substance to contain them if needed . Nina advises Olivia to find Sam Weiss , a man that William Bell had trusted and instructed Nina to also listen to . However , Sam has disappeared and cannot be found . Walter and Peter , along with Massive Dynamic staff , debate how to disable the machine , but Peter realizes that he himself is the only option . Walter comes to recognize that the Observer 's efforts from earlier ( " The Firefly " ) were to prepare him to lose Peter . After preparing himself , Peter goes to touch the machine , but is sent flying by an electrical spark , wounding him and knocking him unconscious . At the hospital chapel , Walter tries to find repentance from God for his actions , while Olivia arrives after hearing the news . She steps outside to observe the sunset when Sam Weiss runs up to her and demands to be taken to the machine to stop what is already happening . 
