If Jesse and Ellie's positions were swapped in the scene when they burst through the theater doors and Abby instantly shoots Jesse in the head without hesitation or even knowing who she was shooting until after the fact. Ellie would have died right there and well I guess that would be it since Jesse would never stand a chance against Abby and Tommy would still be badly injured. Dina would either enter the fray like she does originally and Lev would stop Abby killing her, or Abby just leaves and Dina eventually stumbles across the carnage but can't and won't probably do anything about it because she's pregnant.

Nate's bailed out by Flynn/Lazarevic (likely just Flynn as Lazarevic is the big boss so he doesn't do that kind of task), they take him to Borneo as that's the next stop. When she gets Nate alone Chloe tries to plan how to get him out but it's probably not yet (Nate's likely to be always at gun point by a mook/Flynn/Lazarevic though). They locate the tomb as kind of normal, just with the different situation, find the letter about Nepal, realise the lost fleet didn't have the Cintamani Stone. Since Sully leaves at this point in the original, his exclusion doesn't matter anymore.

Nepal next, with Lazarevic's men causing a ruckus, it could be possible for Nate and Chloe to escape here, find the temple through original means (via rooftop), come across Elena and Jeff, with the original sequence happening along with Jeff death happening as usual. Afterwards the story continues as normal until the epilogue with Sully just absent. If Nate can't get away here, they find the temple through Lazarevic's methods hopefully Elena has is out of the way and not in the path of their search, if not she is sadly executed along with Jeff before they (Nate & Lazareivc's men) go into the temple. Don't want to go into variables so I'll stay with Elena dying here...(possibility of her seeing Nate and wanting to get him out if she survived). Ah I should go into if Nate's witnesses this, he'd definitely try to fight but held back, then refuses to help further but he is in no predicament to do not so he's forced once again to continue, and upset at the loss.

As Nate's the only intelligent one to do puzzles, he does the stuff in the temple albeit at gun point, and probably getting Flynn to help him along with Chloe as if I remember correctly she and Elena helped him in the original with the puzzles. They discover the Stone and Shambhala are in the Himalaya's, so it's on the train! Which....Nate could get away if left with just mooks but he's probably on a tight leash with Flynn or Lazarevic, oh and Draza present. If it's just Draza entrusted with Nate then he can get away, an argument with Chloe wouldn't happen because they didn't spend time with Elena earlier but Flynn can turn up as normal and shoot Nate as he does usually as punishment for killing Draza, Nate could get away again if Chloe stalls Flynn and the story moves on, the crash happens and Nate ends up with Tenzin, yadda yadda. I'll leave it there, because I keep ending up going back to how UC2's original plot goes on once Nate escapes in my version.

OK, if Nate doesn't get away, and if the train journey goes as planned for Lazarevic's men, they end up at Tenzin's village, attack it, which could kill Tenzin and/or Karl if Schafer is even there. So with both of those out, it'll take them even longer to find the caves as they have no local guide and Nate's less useful for that, but he's better than the men. Then again they won't know about the caves so everything takes a heck of a lot longer than it could, eventually finding the entrance to Shambhala. At this point Nate is killed, or perhaps he could get away again if they let him live until they are attacked by the Guardians, so Nate attempts to stop Lazarevic if he's able to escape, I mean he may as well after all the crap he went through.

Yeah there's not much to this game when there's no action in this version apart from maybe the end.

Basically, Nate hands Sully his journal to hold while he swims to the wreckage of a German U-boat (this was shown in the UC4 opening credits) so that it doesn't get wet (despite Drake happily swimming in later games with the journal on him but we won't worry about that). After exploring it and leaving, Drake finds the villains have tracked them down and is forced to share what he found; however, Sully owes the villains money and to teach him a lesson, they threaten to shoot Drake but at the last moment shoot Sully instead, and Drake believes he's dead. Obviously you know this is bullshit because you played the later games where Sully is fine, but it's only because the bullet got blocked by the journal. No journal = Sully's dead.