Basically the outline of the story is that a military dictatorship has basically consumed most of the factions In Seattle with the sole hold out being The fireflies. This dictatorship has a partial cure that is being used to maintain that grip on power. Abby wants to make a permanent cure to undo that grip on power, one that won’t kill Ellie(Because in this version they have a real brain surgeon that can do better then her father), and attempts to kidnap Ellie but accidentally kidnaps Dina. Apparently no longer wanting true revenge on Joel so she just leaves him crippled with a bad leg and steals Dina. Abby then uncovers the truth that Dina isn’t Ellie and uses Dina to lure Ellie.
Abby exposes Dina as a ploy to get Ellie to cooperate and they have to team up to get some of the partial cure. A doctor eventually reconfirms you will have to kill Ellie for this new full cure. So we’re literally just repeating game one. Abby wants it for her people and obviously that’s not cool with the other side so tension ramps back up.
Joel eventually comes to save Ellie, the story rationalizes that they will always come for Ellie for a cure and that they will always turn into a military dictatorship. There is a contrived twist where after saving Dina, someone injects Ellie with a partial cure meaning she no longer has the capacity to create the full cure by harvesting her brain. She blames Joel for still not letting her be her own adult and live her life, Ellie storms off and since Joel can’t catch her he runs off to get revenge on Abby. They fight and he kills Abby but is mortally wounded. It turns out Dina injected Ellie, Ellie runs to Joel, cries as he dies, calls him Dad and such nonsense, and then she goes back to Jackson where she coldly passes Dina who is now the new Joel.
The whole military dictatorship thing is basically pointless and adds nothing of substance and they replace Jessie with a character named Kyle that is Dina’s protective brother who’s arc is basically teen drama level stupid. Who just hates Ellie because she’s not good for her sister and redneck trash and ultimately comes around and shows up to fight off Abby to help Ellie escape and sacrifices himself. We basically lose Jessie and Lev for this trash character.