Another loose end that is tied up in The story is of Corto/ Armitage. WE find that the surreal Armitage mentality is stripped away to reveal the true man beneath all of the augmentations, Corto. It is in a way unfortunate that Corto is killed by Wintermute because he just wants to live, but Wintermute cannot have him running around spilling his secrets.
One part of the story that I do not feel was wrapped up was the part about Flatline Dixie's consciousness. I feel that the story could have done a little better job explaining exactly what happened to him. The story ends with Flatline's consciousness disappearing, thought to be destroyed. But at the very end as the story pans through space, the sound of disembodied laughing is heard. Which is a characteristic of Flatline. Which leads many to believe that Dixie worked out a deal with Neuromancer/Wintermute to exist inside the construct.