Well, I dunno exactly what you’re confused about, but maybe you missed a couple of vital conversations? Here is the general outline (obviously, do NOT read these spoilers before completing the game, anyone, they’d really ruin it):
The Nameless One, before he became nameless and immortal, was a guy who did very, very bad things (just what he did is never specified). Later on, he got intensely regretful, and wanted to make amends. Problem was, he’d never live long enough. So he decided to become immortal, in order to have eternity setting things right.
He enrolled in the Blood War so as to have the chance to go down into the Lower Planes and seek out Ravel, a Night Hag whose power was legendary. He appealed to Ravel’s ego; flattering her and coaxing her until she agreed to make him immortal with a ritual spell.
Once she’d made him immortal (by forcing his mortality apart from him), she tested the spell by killing him. Sure enough, he came back but things didn’t work quite as planned – all his memories were gone.
Since Ravel didn’t know why he’d wanted to become immortal in the first place, she couldn’t tell him, and so the Nameless One just wandered away, all his plans for redemption gone.
Over the centuries, the Nameless One had many adventures, died and lost his memory again many times, and lived every concievable kind of existence. Sometimes he was good, sometimes he was bad. We get little glimpses of these past lives all along; he was the sorcerer who trained Ignus, he was the leader of the rebellion in the Lower Ward and the thief of the Lady’s Key, he was the one who earned the undying hatred of the Mercykillers, he was… all sorts of things. His mortality, meanwhile, gained power along with him, and decided it didn’t like its life or the Nameless One, the one who gave it life, very much.
The most important of the Nameless One’s incarnations from the game’s POV is the Practical Incarnation. He was the one who pulled Morte from the Pillar of Skulls, who rescued Dak’kon from Limbo (for his karach), who got the tattoos on his back and who built the tomb. He was organized. He was the only incarnation (that we know of) to actually succeed in discovering much of his origins. The trail led him to the Fortress of Regrets, where the Nameless One’s mortality; the Transcendent One, had taken up residence.
He failed to defeat the Transcendent One, however, and was killed and lost all his memories again.
The current Nameless One is actually a long time after that one. The Transcendent One has gotten fed up of having him run around and has decided to lure him into the Fortress of Regrets and keep him trapped there forever, or maybe just destroy him once and for all.
The TO therefore has left a trail of clues and people for the Nameless One to find. Once he’s followed the trail, it plans to wipe them all out, so as to make sure no future incarnation will ever find the way to his Fortress again.
Assuming, you get the ‘best’ ending, however, the Nameless One actually forces the TO to unite with him, granting him immense power from all the stored-up experience and knowledge the TO has built up through his link with the NO over all the centuries (millenia). Of course, this makes the Nameless One mortal again, and very overdue for death, but he has time to raise and thank all his companions before he dies.
And when he dies, he wakes up in Hell, back where his journey began; in the middle of the Bloodwar. Because of all the crimes he’s commited throughout his long existence, not to mention the fact that his immortality depended on the death of others. However, it’s not a totally dark ending, as implied by the resigned and calm look on the Nameless One’s face in the final scene. He suggests to some of his companion in their final conversations that his penance will not last forever (although it may be millenia) and perhaps he’ll see some of the more long-lived of them again, some time far away in the future.
~pant, pant~ Of course, that’s just a bare-bones summary. I didn’t even touch on some important stuff, like Deionnara and the Paranoid Incarnation. I’d recommend you just play the game again. You know you want to 