“…What was she doing at the end?”

After awakening from her long slumber in the museum, Vivy witnesses a horrific scene where humans are being massacred by AI. The war between humans and AI has broken out, and amidst the confusion, Vivy meets up with Matsumoto. They recognize that the Singularity Project has been a failure, so they search for Dr. Matsumoto, who was the architect behind the one hundred-year journey, in order to resolve the situation.