she knew he lied to her at the end of the first game which started it. thats why joel has that monologue with tommy in the opening talking about it because he felt guilty and knew she figured it out
She loves Joel enough to go through hell and back She's upset he took meaning out of her life
It is jumbled, melodramatic bullshyt plot points to make the game needlessly dreary
Just like ppl being 1960's type homophobic in 2044. Ellie grew up from 14 to 19 in a damn compound, not on the run or constantly at war.