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The Last of Us - Did You Know Gaming? Feat. Caddicarus
 
In the prologue, if the models of Joel and Tommy were removed, the game will crash after Sarah gets into the car with them, and restarting the checkpoint will allow the player to roam around some areas, from the glitched car to the Louis' burning farm.
Contributed by ProtoSnake
When you unlock all the "Shiv Doors", you'll get a trophy called "Master of Unlocking". This is a reference to Barry Burton's infamous quote to Jill Valentine, when he gave her a lockpick in Resident Evil (1996).
Contributed by ProtoSnake
During development, several of the developers thought the game would ruin Naughty Dog's reputation and tank completely, leading to the studio's downfall. The game eventually wound up winning multiple game of the year awards and was praised by critics and gamers alike.
Contributed by Mass Distraction
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Spoiler:In chapter 7 "Tommy's Dam", when Ellie helps Joel to find a way to cross the dam, Ellie puts her hand up to Joel for a high five, giving the player the choice to high five her or leave her hanging.
This is a reference to The Walking Dead: Season One Episode 3 in the "Travelier Motel", when Duck helps Lee to find what he's looking for, Duck puts his hand up for a high five, giving the player the same choices.
Contributed by ProtoSnake
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In the "Left Behind" DLC, the name of the arcade place "Raja's Arcade" is a reference to Eddy Raja & Rika Raja from Uncharted series. Also it shares the same reference name for "Club Raja" from Uncharted 2: Among Thieves.

When you enter Raja's Arcade you'll find an Jak X: Combat Racing arcade machine from Jak and Daxter series. Once Ellie interacts with it, she'll pretend she's playing while describing the actual gameplay. And once she's done playing and criticizing the game, this awards a trophy named "Nobody's Perfect" with a Jak and Daxter picture. The reason for this is because a lot of Naughty Dog developers weren't happy about the game's success in the past.
Contributed by ProtoSnake
It was revealed during a special one time live event that an extended ending had been written for the game that was never recorded, and went entirely unused. It took place one night after the end of the game, Spoiler: at Tommy's Dam. The scene shows Spoiler:Joel telling Ellie that Tommy is trying to set him up with a girl named Esther, with Ellie acting distant. Joel then begins to play guitar and sing (performed by Joel's actor, Troy Baker). After a joke is told and tension is broken, Joel gifts the guitar to Ellie. The scene would then fade with her strumming a chord. How it all plays out can be disputed, however, as it was only shown to live attendees, which only complicates things, as the game's writer, Neil Druckmann, says that it will never be released in any form. Neil also stated that the scene was intended to Spoiler:be a goodbye for Joel and Ellie, possibly meaning that we may not see them again if a sequel were to be made.
Contributed by totallytman
In Bill's Town, near the graveyard, is a house that highly resembles the house from the beginning of Telltale Games' The Walking Dead.
Contributed by Boyobmas
In the chapter "Pittsburgh" during the "Alone and Forsaken" section, Spoiler:Ellie finally learns how to whistle as she slowly begins to whistle a tune. Ellie is actually whistling the main theme of the Uncharted series, another series created by Naughty Dog.
Contributed by Soulixius
During the opening segment where you play as Spoiler:Joel's daughter, you can find a painting of a lone deer in a snowy forest.
This is foreshadowing later in the game Spoiler:where you play as Ellie in a snowy forest hunting a deer, which is the only other time in the game you don't play as Joel.
Contributed by Boyobmas
The eye exams found on the walls of Spoiler:the Hospital read "RUN YOU R NEARLY THERE DONT QUIT!!"
Contributed by frankfrost2
Three PS3s can be found throughout the game:

• During the opening segment under the TV in the family room.
• On the bottom shelf of a bookcase Spoiler:in a games room in the University.
• In a store Spoiler:while escaping from David's gang in Lakeside Resort.
Contributed by Tuli0hWut
Upon beating the game, Spoiler:you can see Ellie's switchblade lying against the window at the main menu.
Contributed by frankfrost2
Buckley, the dog Joel pets, is named after Troy Baker (The voice of Joel)'s own dog, who died 3 years before the game released.
Contributed by DidYouKnowGaming
The original pitch for the game was called Mankind. In this version, all of the infected would have been women. Ellie would have been the only female to be immune, and Joel was protecting her in order to bring her to a lab to develop a vaccine. The idea was scrapped after several female Naughty Dog employees voiced criticism and concerns over the concept. Neil Druckmann has said that "the reason it failed is because it was a misogynistic idea."
Contributed by Mass Distraction
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Ellie's appearance was revised after the announcement trailer due to a resemblance with the actor Ellen Page.
Contributed by Mass Distraction
At one point during the game's development, Naughty Dog was put under pressure to change Ellie's positioning from the front of the cover art to the background. It is suggested that this was because of the misconception that if you have a female character on the cover, the game will sell less. Naughty Dog refused.
Contributed by Mass Distraction
Naughty Dog had to specifically request female focus testers for the game because they refused to let the game to be tested only on males.
Contributed by Mass Distraction
There was an alternate ending that was cut from the game, but developers showed it at PAX Prime 2013. During filming of the scene, an impromptu song was made to fit the scene, which was played out in full by the actors.
Contributed by Funland47
An enemy which had been scrapped from the final game was an infected elephant which had tendrils of fungus extending from its legs and blooming mushrooms on its head. An encounter with the creature would have Joel, the game's protagonist, scrambling away from it.
Contributed by KnowledgeBase
Before deciding on the fungal infected enemies, early designs of the zombie-like creatures looked like bald, fanged beasts with stringy fungus growing off their back.
Contributed by KnowledgeBase
The cause of the zombie apocalypse is actually based on real life organisms. There is a parasitic fungus called Ophiocordyceps unilateralis, which is known for taking over an ant's mind and controlling its motor skills, basically making it a zombie. In The Last of Us, a fungus takes over most of humanity's minds, and turns them into zombies.
Contributed by JzillaMerida
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The game contains a number on a "Pest Control" poster that is actually a real life sex hotline.
Contributed by DidYouKnowGaming
In the chapter titled "Pittsburg", after you meet two new characters, if you check one of the rooms to the right there will be a Jak and Daxter doll sitting on the dresser, along with a Nathan Drake doll from the Uncharted series on the bed. Also, in the toy store there is a Jak and Daxter and an Uncharted board game sitting on the shelves on the walls oposite to were you entered. Finally, there are four unlockable Jak and Daxter items for Ellie to wear. A T-shirt, hoodie, backpack, and googles. All of these were previous titles made by Naughty Dog.
Contributed by Milkman