The Last of Us has inspired some smart fan theories. As is often the case with most story-driven games, the narrative leads players to concoct their own elaborate explanations, even for elements of the story that weren't mysterious. From ideas that explain Ellie's past to possible crossovers from other video games, The Last of Us fan theories abound.
A big reason for all the fan theories is the moral ambiguity of the game. Joel, the hero, is forced into difficult situations where there's often no obvious answer. Players search for clues and reasons why things turned out the way they did. When there isn't an obvious one, they often come up with their own theories to fill in the holes in just the same way people invent conspiracy theories for confounding events in the real world.
Not every The Last of Us theory is perfectly sound. Some seem pretty ludicrous while others appear to be pretty likely, but that's just the nature of fan theories in a nutshell.
It should go without saying, but there are The Last of Us spoilers ahead.
In the end, Joel saves Ellie by potentially sacrificing the future of the species. Most people see this as a gesture of love and humanity in itself. However, one theory suggests that Joel didn't choose to save Ellie so much as he chose to let humanity die. He's seen firsthand the awfulness of which people are capable. They took his daughter from him, and now they're willing to murder another young girl right in front of him. He doesn't think that humanity deserves the cure that Ellie could provide.
On the surface, it appears that the state of the world in The Last of Us is a pretty clear result of one thing and one thing only, but what if the start of the infection coincided with a massive natural disaster? Something like a massive earthquake and subsequent tsunami would cause a lot of damage and force many people into close quarters. The infection could then spread quickly and exponentially before anyone could do anything to prevent it. This would help explain how conditions deteriorated so quickly.
There's something significant about Ellie's scar, but just what that is remains a mystery. Many people assume it is the product of a school fight or something along those lines, but what if it is actually the source of her immunity? This could work two ways: either she was experimented on and that's a surgical scar, or she had an encounter with an infected at a young age and her body has somehow been fighting it off ever since.
Many of the characters in the game that are supposedly not infected nonetheless exhibit early signs of infection. Specifically, many of the characters lack peripheral vision. This is likely just a way to make stealth gameplay more balanced, but could there be more to it?
It's clear that the infected rely heavily on sound, as the Cordyceps fungus grows over the victims' eyes. It's possible that just about everyone in the game is infected to varying degrees and they just don't know it. Perhaps an airborne strand of the infection is affecting everyone's hearing without turning them into crazies?