"Do not trust corrupted memories."
The things he's seeing might be fabrications of his imagination, false memories inserted into his mind during the process of being 'Projectified', etc.
I think the visions he sees are half-true, half-false. We know Yi's village was murdered and stomped to the ground by Noxian forces... but the shadowy figure obviously has a samurai-themed armor, making it seem like hes Ionian. But why? Why would he see an Ionian in the place of a noxian? Unless... The people who mechanized all these Project champions wanted Yi to believe Ionians are the bad guys.
What if the people behind the PROJECT have connections to Zaun/Noxus, and attempted to make Yi believe Ionians destroyed something dear to him, making him vengeful towards Ionia when it's the place he's supposed to side with?
But Yi escaped with the help of Fiora. And the process was obviously not complete, thus leading to his memories being a complicated mixture of false and true.
This theory goes well with another detail I noticed about the Project skins. You notice how Leona (although not portrayed in the trailer), Fiora and possibly Lucian underneath that scarf, have their face somewhat revealed? And Yi's concept art shows he still has his head and a huge portion of his original body intact underneath the metallic parts. Allow me to quote Riot from the recent Project post:
Artists decided to keep PROJECT skins people-sized, though the champions have fused and augmented their bodies using some big, crazy technology. “In order to become PROJECT you have to surrender your humanity," says Lisa “Saiyaka” Thorn, a visual designer. "The technology takes over your soul."
PROJECT champs aren't just soulless husks, though. Little clues point to their human origin: Yasuo's leather glove, Leona's exposed jaw, Master Yi's wuju-sculpted washboard abs. These aren’t robots—they’re just seriously tricked out people.
They're just tricked out people. Not soulless husks. 'Technology takes over your soul'.
Anyone notice how that applies to all, except... Zed. Zed has no visible human parts in his Project skin- in fact, his face looks completely robotic, it barely even has the shape of a human head anymore. On top of that, he was portrayed as the bad guy in the Project animation, attempting to chase down and eliminate the ones who managed to escape before their Projectification was complete.