On Christmas Eve, 1997, Aya Brea arrives here with her unnamed date, late for one of the plays being shown here. Melissa Pearce, one of the actresses in the play, begins setting the audience on fire; it turns out that she is being possessed by Mitochondria Eve. After the audience and cast burn to death, Aya confronts Eve, unaffected by her mysterious mitochondria powers.
After a battle, Aya follows Eve down a hole. Backstage she sees a little girl wearing hospital clothing that mysteriously vanishes. Aya witnesses a rat transform into a NMC before defeating it in battle. While exploring the area, a heavily burned actress in the dressing room is still alive but soon dies, after tell Aya to stop Mellisa. In another room a clown tries to flee from the area but is killed while trying to escape.
Eventually Aya finds Eve in the rehearsal room playing the piano. Eve transforms into a monster and forces Aya to fight her before Aya, once again, jumps down a hole. This leads to New York's sewers where she encounters more transformed enemies. At the end, she fights the first boss of the game, the Alligator.
After its death, she leaves and is accosted by a reporter but was the interview abruptly ends with the entry of Daniel Dollis. Carnegie Hall becomes inaccessible after that.
After the events in the game transpire, she, along with her friends tried to make up for a lost Christmas by going to the opera at Carnegie Hall once again, which has been repaired from the fire damage and corpses. During this time, Aya communicates with the entire audience's mitochondria and their eyes begin to glow a pinkish red.
- If Aya doesn't jump down the first hole, she can head back out to the entrance of Carnegie Hall and receive a lot of handgun ammunition from a police officer.
- Inside the store room on the left wall of backstage, examine the closet to find the rat and examine it again to get a handgun. Also examine the wall on the left to get a secret armor.
- During the sewer, after Maya opens a locked door Aya can run to the right to explore a secret room.
- In The 3rd Birthday, "Aya" can find a poster of a "famous New York Opera house", and she feels she has bad memories about the place.
|Aya Brea - Daniel Dollis - Kunihiko Maeda - Melissa Pearce - Mitochondria Eve|
Maya Brea - Ben Dollis - Lorraine Dollis - Hans Klamp - Douglas Baker - Torres Owens - Wayne Garcia
|Armadillo - Bacterium - Bat - Bear - Cat - Centipede - Chameleon - Crow - Dogman - Flyman - Frog - Mixedman - Mole - Monkey - Parrot - Plant - Pterodactyl - Rat - Ratman - Spider - Scorpion - Squirrel - Snake - Treasurebox - Troodon|
|Alligator - Bee - Cockroach - Crab - Eve - Giantworm - Kerberos - Spiderwoman - Triceratops - Truebred Eve - T-Rex - Ultimate Being|
|American Museum of Natural History - Carnegie Hall - Central Park - Chinatown - Chrysler Building - N.Y.P.D. - Soho - St. Francis Hospital - Subway - Warehouse|
|Weapons - Soundtrack - Remixes Soundtrack|