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This is probably the best article there is regarding The Last Of Us' AI (and answers your question of "how did I know", Jay50)

http://venturebeat.com/2012/06/08/the-last-of-us-is-even-smarter-than-you-think/

In a more dangerous situation, however, every single dynamic takes on major significance. When they’re discovered, Joel pulls out his revolver. Instantly, a scavenger warns his friends: “Aw, shit! He’s got a gun!”

“How many did you see?”

“Only saw one! He’s right by the door!” And yes, that’s right where Joel’s hiding. When he fires his gun, Ellie jumps, covering her ears. One of the scavengers gets the jump on Joel, bashing him up and adding a nasty cut across Joel’s nose before putting him in a choke hold for the men aiming from the windows. They take their time, making sure they hit Joel and not their friend.

At times like these, we’ve seen Ellie jump in before, using her butterfly knife to stick someone who’s got Joel on the ropes. This time, nothing … because those gunmen at the windows will take her out if she tries, and she knows it. Naughty Dog built a survival instinct into Ellie. It’s so good, Naughty Dog decided that players didn’t need the ability to direct her. Ellie directs herself.