Here is the story line according to John Byrne
"I'm going to break one of my own rules here, since I have, at one time or another, discussed most of the details of Mariko's death as I had worked it out. So here it is all together, for those who haven't seen it before (and even those who have):
Sabretooth attacks Mariko as a way of getting to Wolverine. He brutalizes her beyond imagining. (Nothing sexual. This is sheer animal violence.) He leaves her for dead, torn and bleeding in a alley.
But she isn't dead, and the X-Men, tracking Sabretooth, find her. They race her to a hospital, and over the next several issues she lies in a coma, on life support. Other things occupy the X-Men's time for a while, but their thoughts keep coming back to Mariko. Wolverine returns to her bedside as often as he can. Her condition remains unchanged.
Finally, he can take it no longer. He begs Jean and Xavier to do something, to save her. Xavier scans her and makes a sad discovery. She is brain dead. Only the machines are keeping her alive.
Wolverine refuses to believe it. But Jean links his mind to Mariko, and he feels the emptiness where her soul used to be. He asks to be left alone with her.
Xavier and Jean depart, to wait outside. Wolverine sits by Mariko's beside, holding her hand, stroking her hair. He rises. He looks at the machines that are maintaining her life functions. In a sudden, swift movement he pops his claws and slashes the power cables. The machines fizzle and shut down.
Outside, in the hall, Jean and X have both "felt" what has happened. They move toward the door, but Wolverine comes out before they can enter. He stands for a moment in silence, looking at them. Finally he speaks. "She ain't meat," he says softly. And in an instant, he is gone, disappearing down a stairway.
Next issue, he finds and, in the most horrifying battle the Code would allow, kills Sabretooth (who was, at this point, to be revealed as his father.) " It is a shame he left the book, although his Fantastic Four is beyond awesome.