The Firefly Lab is the second-to-last chapter, set inside Saint Mary's Hospital in Salt Lake City, where the Fireflies have their base. It is a single section played as Joel, and its five collectibles include the recordings that explain what the Fireflies have learned from Ellie.
Part 11 of 12 in Main story
The Hospital is the only section. It starts with Joel waking in a hospital bed, moves up through the building to the sixth floor and the operating room, and ends down in the parking garage.
Joel comes to with Marlene at his bedside, who apologizes for the knock on the head and asks how they made it. He tells her Ellie fought hard to get there and asks to see her. Everything after this conversation is a major story spoiler.
Marlene explains that the infection in Ellie's brain has mutated, which is why she is immune, and that the doctors want to study it to make a vaccine. Joel realizes the surgery will kill her. Marlene has a guard, Ethan, walk Joel out with orders to shoot if he tries anything. Joel disarms him, forces out that the operating room is on the top floor, and kills him.
The Fireflies are now the enemy, and you can sneak past or fight them floor by floor, sealing off the West Wing on the way. On the top floor the recordings reveal the surgeon's view of Ellie's immunity and Marlene's doubts about sacrificing a girl she promised to protect. Joel bursts into the operating room, kills the head surgeon, Jerry Anderson, when he blocks the way, and carries Ellie to the elevator.
Marlene is waiting in the parking garage and tries to talk Joel into handing Ellie back. He shoots her, puts Ellie in a car, and then kills Marlene as she pleads, saying she would only come after Ellie. Driving out, he tells a waking Ellie that there were many immune people and that the Fireflies have given up on a cure.
Image: Naughty Dog / PlayStationLakeside Resort
Lakeside Resort jumps to winter and puts you in control of Ellie near Silver Lake, Colorado, hunting with a bow and searching for medicine. She runs into two strangers, David and James, and for part of the second half the game switches you back to Joel.
Image: Naughty Dog / PlayStationThe Quarantine Zone
The Quarantine Zone starts the story proper 20 years after the outbreak, inside Boston's military-run zone in August 2033. As Joel, now a smuggler, you and his partner Tess slip outside the wall to track down Robert, a dealer who owes them guns, and end up taking a new job from the Fireflies.
Image: Naughty Dog / PlayStationBus Depot
Bus Depot opens in the spring of 2034 as Joel and Ellie walk into Salt Lake City, aiming for the Fireflies at Saint Mary's Hospital. The route runs along a highway full of dead cars, through the Logan James bus station and an abandoned quarantine zone, and down into a flooded tunnel full of infected.
Mallrats
Mallrats is the second chapter of Left Behind and the first full flashback: Ellie and Riley dodge a patrol in Boston, cross the rooftops and slip into the abandoned Liberty Gardens mall. It is a calm, story-driven chapter with Halloween masks, a brick-throwing contest that unlocks a trophy, and a breaker switch that brings the mall's lights back.