- Amaya Heller: "I miss you daddy."
- James Heller: "I miss you too baby girl, but don't worry, daddy's coming home."
- ―Amaya and James Heller.[src]
During this time there was a viral outbreak, resulting in infection and deaths. Blackwatch, a military organization had quarantined the city. A group of Infected are said to have barged into Heller's residence and killed her mother along with supposedly killing Amaya.
When Heller enters the Red Zone, he discovers that Amaya is indeed alive, but captured by an unknown governmental bureau. Heller eventually returns to Dana's safe house and sees on a broadcast across all NYZ that Rooks has her held captive at Gentek HQ. When Heller arrives, Rooks kills two Blackwatch soldiers and he allows Heller to save Amaya.
Heller immediately enters the room where she is being held hostage by Sabrina Galloway. Galloway then escapes the building and is taking Amaya to Mercer. After Heller defeats and consumes Mercer, it is revealed that she and Dana are stored in a bank vault. Heller finds them, Dana is happy to see Heller, but Amaya becomes scared of her father due to showing his infected powers. In the ending she appears next to Dana. Heller, believing that he has no place in his daughter's life attempted to leave the building but is stopped by Amaya and the two embrace.