The Plot behind the Assassinations
In the end when you finally meet Letho he explains to you that he fulfilled the plan developed by Emhyr var Emreis to "soften" the North before the upcoming invasion.
You can either kill Letho or let him live. You don't gain anything by killing him though, but you can have "the final battle" which is compulsory for many games.
If you spare him, then as the journal says his fate is "story for another time".
- Notice in the final cutscene, Geralt gets slashed in the side during a pirouette strike - this may be an acknowledgement to an earlier conversation in the first game, with Berengar, who mentions how Geralt leaves it open during the move.
Geralt and Triss (Roche's Path)
If Geralt chose to save Triss, after defeating the dragon she meets him on the wall and says that Letho is waiting at the main square. Later they meet Roche who is declared a criminal in the Northern Kingdoms. He is not pleased that Geralt didn't help him save Anaïs and that Dethmold could escape.
Vernon serves Redania (Roche's Path)
If Geralt chooses to save Anaïs, then after defeating the dragon Vernon Roche meets him on the wall and tells him that Letho is waiting at the main square. If after For Temeria! quest you advised Roche to give Anaïs to Radovid, then he wears a Redanian uniform and tells you that he now serves King Radovid. If, however, you convinced him to give the girl over to John Natalis, he'll remark that she'll make a great queen one day and when Natalis tried to give her a doll she refused, asking for a sword instead as she wanted to learn how to fight.
When you meet Letho on the main square you finally meet Triss. She tells you that Letho saved her from Nilfgaardians and then from soldiers that started killing mages and raping sorceresses after the chaos caused by the dragon erupted.