For the complete The Last of Us: Left Behind experience, read Prima's free walkthrough.
An opening cut scene lets us know that the events of Left Behind take place in the middle of the original game, just after The University chapter. It also introduces players to Riley, a friend of Ellie's who she knew prior to the original story.
When you gain control of Ellie, head up escalator in front of you and run straight ahead. You'll hear the distant sounds of a Clicker. Ignore them and head right towards Weston's Pharmacy. Crouch so you can crawl under the gate. There's no opposition in the pharmacy, so check the entire room for parts that you can use to craft items. Head behind the counter to the right of where you entered. Ellie will spot a first aid kit in another room, but can't get there. Pick up the Combination Note on the ground near the counter and head out the way you entered the pharmacy.
Just to the right of Weston's Pharmacy is the American Princess store. When you approach it, Ellie will use the combination found in the note to open the gate. There are spores inside but no opposition. Find the pharmacist in the back corner of the room and get the Pharmacy Key. This is not one of the Artifacts you need to find, as it is given to you through the progression of the story. Before you leave, be sure to grab the Pharmacist's Note in the same location.
Head back the same way you came but don't go outside just yet, there's a Clicker waiting for you. Press R2 to focus Ellie's hearing. Grab a nearby brick and when the Clicker passes, crawl under the door. Use the brick to distract the Clicker, making your way back to Weston's Pharmacy. Go back behind the same counter where you found the Combination Note and through the locked door. Once Ellie checks the first aid kit, head out the window.
Head forward into the store just to the right. If you try to crawl through the gap just in front of you, the debris will fall, closing it off. When you enter the store, head to the right and crawl through another gap. Check the area for items that can be used for crafting before heading to the right and navigating through the debris. Grab the supplies from the dead medic and pick up the Salon Note near his body.
When you leave the store, go down the stairs and vault over the railing, ending the first chapter, Back in a Flash.