Some bad guys blow up Wolverine’s brain by putting a bomb in his mouth, leaving him “brain dead.” Doctor Strange arrives.
Doctor Strange examines him and says that the bomb took away Logan’s soul. Strange visits Wolverine on the astral plane…
…Which looks like a bar to Logan. Strange then tells Wolverine that he’s died a bunch of times, and each time he has to defeat the angel of death to return to life.
This becomes the basis for exploring events in Logan’s past, like when he was part of Weapon X and the time Magneto ripped out his adamantium, until he realizes that when Gorgon killed him and the Hand’s operative, named Phaedra, brought him back to life, they kept a little piece of him.
So, Wolverine wills himself back into his body and sets out to kill Phaedra. But when he reaches her he finds Lord Shingen, Mariko’s father. Logan takes out Shingen and kills Phaedra, reclaims his soul, and the angel of death tells him that the next time he dies, he won’t be able to come back.
Of course, those of us who read the extended “Death of Logan” storyline several years ago know that’s not true…